BioBB ANALYSIS Command Line Help

Generic usage:

biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>

---

Cpptraj_average

Wrapper of the Ambertools Cpptraj module for calculating a structure average of a given cpptraj compatible trajectory.

Get help

Command:

cpptraj_average -h

usage: cpptraj_average [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH -o OUTPUT_CPPTRAJ_PATH

Calculates a structure average of a given cpptraj compatible trajectory.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  -o OUTPUT_CPPTRAJ_PATH, --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed structure. Accepted formats: mdcrd, crd, netcdf, nc, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP

• input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB

• output_cpptraj_path (string): Path to the output processed structure. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• start (integer): (1) Starting frame for slicing..

• end (integer): (-1) Ending frame for slicing..

• steps (integer): (1) Step for slicing..

• mask (string): (all-atoms) Mask definition. .

• format (string): (netcdf) Output trajectory format. .

• binary_path (string): (cpptraj) Path to the cpptraj executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (afandiadib/ambertools:serial) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  end: -1
  format: pdb
  mask: c-alpha
  start: 1
  steps: 1

Docker config file

properties:
  container_image: afandiadib/ambertools:serial
  container_path: docker
  container_volume_path: /tmp
  end: -1
  format: pdb
  mask: c-alpha
  start: 1
  steps: 1

Singularity config file

properties:
  container_image: shub://bioexcel/ambertools_singularity
  container_path: singularity
  container_volume_path: /tmp
  end: -1
  format: pdb
  mask: c-alpha
  start: 1
  steps: 1

Command line

cpptraj_average --config config_cpptraj_average.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.average.pdb

JSON

Common config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "pdb"
  }
}

Docker config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "pdb",
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}

Singularity config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "pdb",
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

cpptraj_average --config config_cpptraj_average.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.average.pdb

Cpptraj_bfactor

Wrapper of the Ambertools Cpptraj module for calculating the Bfactor fluctuations of a given cpptraj compatible trajectory.

Get help

Command:

cpptraj_bfactor -h

usage: cpptraj_bfactor [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH [--input_exp_path INPUT_EXP_PATH] -o OUTPUT_CPPTRAJ_PATH

Calculates the Bfactor fluctuations of a given cpptraj compatible trajectory.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  -o OUTPUT_CPPTRAJ_PATH, --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed analysis. Accepted formats: dat, agr, xmgr, gnu.

optional arguments:
  --input_exp_path INPUT_EXP_PATH
                        Path to the experimental reference file (required if reference = experimental). Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP

• input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB

• input_exp_path (string): Path to the experimental reference file (required if reference = experimental). File type: input. Sample file. Accepted formats: PDB

• output_cpptraj_path (string): Path to the output processed analysis. File type: output. Sample file. Accepted formats: DAT, AGR, XMGR, GNU

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• start (integer): (1) Starting frame for slicing.

• end (integer): (-1) Ending frame for slicing.

• steps (integer): (1) Step for slicing.

• mask (string): (all-atoms) Mask definition. .

• reference (string): (first) Reference definition. .

• binary_path (string): (cpptraj) Path to the cpptraj executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (afandiadib/ambertools:serial) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  end: -1
  mask: c-alpha
  reference: first
  start: 1
  steps: 1

Command line

cpptraj_bfactor --config config_cpptraj_bfactor.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --input_exp_path experimental.1e5t.pdb --output_cpptraj_path ref_cpptraj.bfactor.first.dat

JSON

Common config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "reference": "first"
  }
}

Command line

cpptraj_bfactor --config config_cpptraj_bfactor.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --input_exp_path experimental.1e5t.pdb --output_cpptraj_path ref_cpptraj.bfactor.first.dat

Cpptraj_convert

Wrapper of the Ambertools Cpptraj module for converting between cpptraj compatible trajectory file formats and/or extracting a selection of atoms or frames.

Get help

Command:

cpptraj_convert -h

usage: cpptraj_convert [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH -o OUTPUT_CPPTRAJ_PATH

Converts between cpptraj compatible trajectory file formats and/or extracts a selection of atoms or frames.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  -o OUTPUT_CPPTRAJ_PATH, --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed trajectory. Accepted formats: mdcrd, crd, netcdf, nc, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP

• input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB

• output_cpptraj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• start (integer): (1) Starting frame for slicing.

• end (integer): (-1) Ending frame for slicing.

• steps (integer): (1) Step for slicing.

• mask (string): (all-atoms) Mask definition. .

• format (string): (netcdf) Output trajectory format. .

• binary_path (string): (cpptraj) Path to the cpptraj executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (afandiadib/ambertools:serial) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Docker config file

properties:
  container_image: afandiadib/ambertools:serial
  container_path: docker
  container_volume_path: /tmp
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Singularity config file

properties:
  container_image: shub://bioexcel/ambertools_singularity
  container_path: singularity
  container_volume_path: /tmp
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Command line

cpptraj_convert --config config_cpptraj_convert.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.convert.netcdf

JSON

Common config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf"
  }
}

Docker config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf",
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}

Singularity config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf",
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

cpptraj_convert --config config_cpptraj_convert.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.convert.netcdf

Cpptraj_dry

Wrapper of the Ambertools Cpptraj module for dehydrating a given cpptraj compatible trajectory stripping out solvent molecules and ions.

Get help

Command:

cpptraj_dry -h

usage: cpptraj_dry [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH -o OUTPUT_CPPTRAJ_PATH

Dehydrates a given cpptraj compatible trajectory stripping out solvent molecules and ions.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  -o OUTPUT_CPPTRAJ_PATH, --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed trajectory. Accepted formats: mdcrd, crd, netcdf, nc, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP

• input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB

• output_cpptraj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• start (integer): (1) Starting frame for slicing..

• end (integer): (-1) Ending frame for slicing..

• steps (integer): (1) Step for slicing..

• mask (string): (all-atoms) Mask definition. .

• format (string): (netcdf) Output trajectory format. .

• binary_path (string): (cpptraj) Path to the cpptraj executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (afandiadib/ambertools:serial) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Docker config file

properties:
  container_image: afandiadib/ambertools:serial
  container_path: docker
  container_volume_path: /tmp
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Singularity config file

properties:
  container_image: shub://bioexcel/ambertools_singularity
  container_path: singularity
  container_volume_path: /tmp
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Command line

cpptraj_dry --config config_cpptraj_dry.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.dry.netcdf

JSON

Common config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf"
  }
}

Docker config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf",
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}

Singularity config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf",
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

cpptraj_dry --config config_cpptraj_dry.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.dry.netcdf

Cpptraj_image

Wrapper of the Ambertools Cpptraj module for correcting periodicity (image) from a given cpptraj trajectory file.

Get help

Command:

cpptraj_image -h

usage: cpptraj_image [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH -o OUTPUT_CPPTRAJ_PATH

Corrects periodicity (image) from a given cpptraj trajectory file.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  -o OUTPUT_CPPTRAJ_PATH, --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed trajectory. Accepted formats: mdcrd, crd, netcdf, nc, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP

• input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB

• output_cpptraj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• start (integer): (1) Starting frame for slicing..

• end (integer): (-1) Ending frame for slicing..

• steps (integer): (1) Step for slicing..

• mask (string): (all-atoms) Mask definition. .

• format (string): (netcdf) Output trajectory format. .

• binary_path (string): (cpptraj) Path to the cpptraj executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (afandiadib/ambertools:serial) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Docker config file

properties:
  container_image: afandiadib/ambertools:serial
  container_path: docker
  container_volume_path: /tmp
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Singularity config file

properties:
  container_image: shub://bioexcel/ambertools_singularity
  container_path: singularity
  container_volume_path: /tmp
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Command line

cpptraj_image --config config_cpptraj_image.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.image.netcdf

JSON

Common config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf"
  }
}

Docker config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf",
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}

Singularity config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf",
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

cpptraj_image --config config_cpptraj_image.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.image.netcdf

Cpptraj_mask

Wrapper of the Ambertools Cpptraj module for extracting a selection of atoms from a given cpptraj compatible trajectory.

Get help

Command:

cpptraj_mask -h

usage: cpptraj_mask [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH -o OUTPUT_CPPTRAJ_PATH

Extracts a selection of atoms from a given cpptraj compatible trajectory.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  -o OUTPUT_CPPTRAJ_PATH, --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed trajectory. Accepted formats: mdcrd, crd, netcdf, nc, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP

• input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB

• output_cpptraj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• start (integer): (1) Starting frame for slicing..

• end (integer): (-1) Ending frame for slicing..

• steps (integer): (1) Step for slicing..

• mask (string): (all-atoms) Mask definition. .

• format (string): (netcdf) Output trajectory format. .

• binary_path (string): (cpptraj) Path to the cpptraj executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (afandiadib/ambertools:serial) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Docker config file

properties:
  container_image: afandiadib/ambertools:serial
  container_path: docker
  container_volume_path: /tmp
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Singularity config file

properties:
  container_image: shub://bioexcel/ambertools_singularity
  container_path: singularity
  container_volume_path: /tmp
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Command line

cpptraj_mask --config config_cpptraj_mask.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.mask.netcdf

JSON

Common config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf"
  }
}

Docker config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf",
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}

Singularity config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf",
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

cpptraj_mask --config config_cpptraj_mask.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.mask.netcdf

Cpptraj_rgyr

Wrapper of the Ambertools Cpptraj module for computing the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.

Get help

Command:

cpptraj_rgyr -h

usage: cpptraj_rgyr [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH -o OUTPUT_CPPTRAJ_PATH

Computes the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  -o OUTPUT_CPPTRAJ_PATH, --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output analysis. Accepted formats: dat, agr, xmgr, gnu.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP

• input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB

• output_cpptraj_path (string): Path to the output analysis. File type: output. Sample file. Accepted formats: DAT, AGR, XMGR, GNU

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• start (integer): (1) Starting frame for slicing..

• end (integer): (-1) Ending frame for slicing..

• steps (integer): (1) Step for slicing..

• mask (string): (all-atoms) Mask definition. .

• binary_path (string): (cpptraj) Path to the cpptraj executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (afandiadib/ambertools:serial) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  end: -1
  mask: c-alpha
  start: 1
  steps: 1

Docker config file

properties:
  container_image: afandiadib/ambertools:serial
  container_path: docker
  container_volume_path: /tmp
  end: -1
  mask: c-alpha
  start: 1
  steps: 1

Singularity config file

properties:
  container_image: shub://bioexcel/ambertools_singularity
  container_path: singularity
  container_volume_path: /tmp
  end: -1
  mask: c-alpha
  start: 1
  steps: 1

Command line

cpptraj_rgyr --config config_cpptraj_rgyr.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.rgyr.dat

JSON

Common config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha"
  }
}

Docker config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}

Singularity config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

cpptraj_rgyr --config config_cpptraj_rgyr.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.rgyr.dat

Cpptraj_rms

Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.

Get help

Command:

cpptraj_rms -h

usage: cpptraj_rms [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH [--input_exp_path INPUT_EXP_PATH] --output_cpptraj_path OUTPUT_CPPTRAJ_PATH [--output_traj_path OUTPUT_TRAJ_PATH]

Calculates the Root Mean Square deviation (RMSd) of a given cpptraj compatible trajectory.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed analysis. Accepted formats: dat, agr, xmgr, gnu.

optional arguments:
  --input_exp_path INPUT_EXP_PATH
                        Path to the experimental reference file (required if reference = experimental). Accepted formats: pdb.
  --output_traj_path OUTPUT_TRAJ_PATH
                        Path to the output processed trajectory. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP

• input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB

• input_exp_path (string): Path to the experimental reference file (required if reference = experimental). File type: input. Sample file. Accepted formats: PDB

• output_cpptraj_path (string): Path to the output processed analysis. File type: output. Sample file. Accepted formats: DAT, AGR, XMGR, GNU

• output_traj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• start (integer): (1) Starting frame for slicing.

• end (integer): (-1) Ending frame for slicing.

• steps (integer): (1) Step for slicing.

• mask (string): (all-atoms) Mask definition. .

• reference (string): (first) Reference definition. .

• nofit (boolean): (False) Do not perform best-fit RMSD.

• norotate (boolean): (False) Translate but do not rotate coordinates.

• nomod (boolean): (False) Do not modify coordinates.

• binary_path (string): (cpptraj) Path to the cpptraj executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (afandiadib/ambertools:serial) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  end: -1
  mask: c-alpha
  reference: first
  start: 1
  steps: 1

Command line

cpptraj_rms --config config_cpptraj_rms.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --input_exp_path experimental.1e5t.pdb --output_cpptraj_path ref_cpptraj.rms.first.dat --output_traj_path cpptraj.traj.dcd

JSON

Common config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "reference": "first"
  }
}

Command line

cpptraj_rms --config config_cpptraj_rms.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --input_exp_path experimental.1e5t.pdb --output_cpptraj_path ref_cpptraj.rms.first.dat --output_traj_path cpptraj.traj.dcd

Cpptraj_rmsf

Wrapper of the Ambertools Cpptraj module for calculating the Root Mean Square fluctuations (RMSf) of a given cpptraj compatible trajectory.

Get help

Command:

cpptraj_rmsf -h

usage: cpptraj_rmsf [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH [--input_exp_path INPUT_EXP_PATH] -o OUTPUT_CPPTRAJ_PATH

Calculates the Root Mean Square fluctuations (RMSf) of a given cpptraj compatible trajectory.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  -o OUTPUT_CPPTRAJ_PATH, --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed analysis. Accepted formats: dat, agr, xmgr, gnu.

optional arguments:
  --input_exp_path INPUT_EXP_PATH
                        Path to the experimental reference file (required if reference = experimental). Accepted formats: pdb.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP

• input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB

• input_exp_path (string): Path to the experimental reference file (required if reference = experimental). File type: input. Sample file. Accepted formats: PDB

• output_cpptraj_path (string): Path to the output processed analysis. File type: output. Sample file. Accepted formats: DAT, AGR, XMGR, GNU

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• start (integer): (1) Starting frame for slicing.

• end (integer): (-1) Ending frame for slicing.

• steps (integer): (1) Step for slicing.

• mask (string): (all-atoms) Mask definition. .

• reference (string): (first) Reference definition. .

• binary_path (string): (cpptraj) Path to the cpptraj executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (afandiadib/ambertools:serial) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  end: -1
  mask: c-alpha
  reference: first
  start: 1
  steps: 1

Command line

cpptraj_rmsf --config config_cpptraj_rmsf.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --input_exp_path experimental.1e5t.pdb --output_cpptraj_path ref_cpptraj.rmsf.first.dat

JSON

Common config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "reference": "first"
  }
}

Command line

cpptraj_rmsf --config config_cpptraj_rmsf.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --input_exp_path experimental.1e5t.pdb --output_cpptraj_path ref_cpptraj.rmsf.first.dat

Cpptraj_slice

Wrapper of the Ambertools Cpptraj module for extracting a particular trajectory slice from a given cpptraj compatible trajectory.

Get help

Command:

cpptraj_slice -h

usage: cpptraj_slice [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH -o OUTPUT_CPPTRAJ_PATH

Extracts a particular trajectory slice from a given cpptraj compatible trajectory.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  -o OUTPUT_CPPTRAJ_PATH, --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed trajectory. Accepted formats: mdcrd, crd, netcdf, nc, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP

• input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB

• output_cpptraj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• start (integer): (1) Starting frame for slicing..

• end (integer): (-1) Ending frame for slicing..

• steps (integer): (1) Step for slicing..

• mask (string): (all-atoms) Mask definition. .

• format (string): (netcdf) Output trajectory format. .

• binary_path (string): (cpptraj) Path to the cpptraj executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (afandiadib/ambertools:serial) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  end: 20
  format: netcdf
  mask: c-alpha
  start: 2
  steps: 2

Docker config file

properties:
  container_image: afandiadib/ambertools:serial
  container_path: docker
  container_volume_path: /tmp
  end: 20
  format: netcdf
  mask: c-alpha
  start: 2
  steps: 2

Singularity config file

properties:
  container_image: shub://bioexcel/ambertools_singularity
  container_path: singularity
  container_volume_path: /tmp
  end: 20
  format: netcdf
  mask: c-alpha
  start: 2
  steps: 2

Command line

cpptraj_slice --config config_cpptraj_slice.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.slice.netcdf

JSON

Common config file

{
  "properties": {
    "start": 2,
    "end": 20,
    "steps": 2,
    "mask": "c-alpha",
    "format": "netcdf"
  }
}

Docker config file

{
  "properties": {
    "start": 2,
    "end": 20,
    "steps": 2,
    "mask": "c-alpha",
    "format": "netcdf",
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}

Singularity config file

{
  "properties": {
    "start": 2,
    "end": 20,
    "steps": 2,
    "mask": "c-alpha",
    "format": "netcdf",
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

cpptraj_slice --config config_cpptraj_slice.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.slice.netcdf

Cpptraj_snapshot

Wrapper of the Ambertools Cpptraj module for extracting a particular snapshot from a given cpptraj compatible trajectory.

Get help

Command:

cpptraj_snapshot -h

usage: cpptraj_snapshot [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH -o OUTPUT_CPPTRAJ_PATH

Extracts a particular snapshot from a given cpptraj compatible trajectory.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  -o OUTPUT_CPPTRAJ_PATH, --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed structure. Accepted formats: mdcrd, crd, netcdf, nc, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP

• input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB

• output_cpptraj_path (string): Path to the output processed structure. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• snapshot (integer): (1) Frame to be captured for snapshot.

• mask (string): (all-atoms) Mask definition. .

• format (string): (netcdf) Output trajectory format. .

• binary_path (string): (cpptraj) Path to the cpptraj executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (afandiadib/ambertools:serial) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  format: pdb
  mask: c-alpha
  snapshot: 12

Docker config file

properties:
  container_image: afandiadib/ambertools:serial
  container_path: docker
  container_volume_path: /tmp
  format: pdb
  mask: c-alpha
  snapshot: 12

Singularity config file

properties:
  container_image: shub://bioexcel/ambertools_singularity
  container_path: singularity
  container_volume_path: /tmp
  format: pdb
  mask: c-alpha
  snapshot: 12

Command line

cpptraj_snapshot --config config_cpptraj_snapshot.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.snapshot.pdb

JSON

Common config file

{
  "properties": {
    "snapshot": 12,
    "mask": "c-alpha",
    "format": "pdb"
  }
}

Docker config file

{
  "properties": {
    "snapshot": 12,
    "mask": "c-alpha",
    "format": "pdb",
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}

Singularity config file

{
  "properties": {
    "snapshot": 12,
    "mask": "c-alpha",
    "format": "pdb",
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

cpptraj_snapshot --config config_cpptraj_snapshot.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.snapshot.pdb

Cpptraj_strip

Wrapper of the Ambertools Cpptraj module for stripping a defined set of atoms (mask) from a given cpptraj compatible trajectory.

Get help

Command:

cpptraj_strip -h

usage: cpptraj_strip [-h] [-c CONFIG] --input_top_path INPUT_TOP_PATH --input_traj_path INPUT_TRAJ_PATH -o OUTPUT_CPPTRAJ_PATH

Strips a defined set of atoms (mask) from a given cpptraj compatible trajectory.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the input trajectory to be processed. Accepted formats: mdcrd, crd, cdf, netcdf, nc, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
  -o OUTPUT_CPPTRAJ_PATH, --output_cpptraj_path OUTPUT_CPPTRAJ_PATH
                        Path to the output processed trajectory. Accepted formats: mdcrd, crd, netcdf, nc, rst7, ncrst, dcd, pdb, mol2, binpos, trr, xtc, sqm.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_top_path (string): Path to the input structure or topology file. File type: input. Sample file. Accepted formats: TOP, PDB, PRMTOP, PARMTOP, ZIP

• input_traj_path (string): Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: MDCRD, CRD, CDF, NETCDF, NC, RESTART, NCRESTART, RESTARTNC, DCD, CHARMM, COR, PDB, MOL2, TRR, GRO, BINPOS, XTC, CIF, ARC, SQM, SDF, CONFLIB

• output_cpptraj_path (string): Path to the output processed trajectory. File type: output. Sample file. Accepted formats: MDCRD, CRD, NETCDF, NC, RST7, NCRST, DCD, PDB, MOL2, BINPOS, TRR, XTC, SQM

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• start (integer): (1) Starting frame for slicing..

• end (integer): (-1) Ending frame for slicing..

• steps (integer): (1) Step for slicing..

• mask (string): (all-atoms) Mask definition. .

• format (string): (netcdf) Output trajectory format. .

• binary_path (string): (cpptraj) Path to the cpptraj executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (afandiadib/ambertools:serial) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Docker config file

properties:
  container_image: afandiadib/ambertools:serial
  container_path: docker
  container_volume_path: /tmp
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Singularity config file

properties:
  container_image: shub://bioexcel/ambertools_singularity
  container_path: singularity
  container_volume_path: /tmp
  end: -1
  format: netcdf
  mask: c-alpha
  start: 1
  steps: 1

Command line

cpptraj_strip --config config_cpptraj_strip.yml --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.strip.netcdf

JSON

Common config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf"
  }
}

Docker config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf",
    "container_path": "docker",
    "container_image": "afandiadib/ambertools:serial",
    "container_volume_path": "/tmp"
  }
}

Singularity config file

{
  "properties": {
    "start": 1,
    "end": -1,
    "steps": 1,
    "mask": "c-alpha",
    "format": "netcdf",
    "container_path": "singularity",
    "container_image": "shub://bioexcel/ambertools_singularity",
    "container_volume_path": "/tmp"
  }
}

Command line

cpptraj_strip --config config_cpptraj_strip.json --input_top_path cpptraj.parm.top --input_traj_path cpptraj.traj.dcd --output_cpptraj_path ref_cpptraj.strip.netcdf

Gmx_check

Wrapper of the GROMACS check module for comparing and validating GROMACS files.

Get help

Command:

gmx_check -h

/bin/sh: 1: gmx_check: not found

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_structure_path (string): Path to the first GROMACS run input file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT

• input_structure_2_path (string): Path to the second GROMACS run input file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT

• input_traj_path (string): Path to the first GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG

• input_traj_2_path (string): Path to the second GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG

• input_energy_path (string): Path to the first GROMACS energy file. File type: input. Sample file. Accepted formats: EDR

• input_energy_2_path (string): Path to the second GROMACS energy file. File type: input. Sample file. Accepted formats: EDR

• structure_check_path (string): Path to the structure file to analyze for internal consistency. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT

• input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX

• output_log_path (string): Path to the text file storing the gmx check console output. File type: output. Sample file. Accepted formats: TXT, LOG, OUT

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• vdwfac (number): (0.8) Fraction of the sum of Van der Waals radii used as warning cutoff..

• bonlo (number): (0.4) Minimum fraction of the sum of Van der Waals radii for bonded atoms..

• bonhi (number): (0.7) Maximum fraction of the sum of Van der Waals radii for bonded atoms..

• relative_tolerance (number): (0.001) Relative tolerance for comparing real values..

• absolute_tolerance (number): (0.001) Absolute tolerance, useful when sums are close to zero..

• rmsd (boolean): (False) Print RMSD for coordinates, velocities and forces..

• compare_ab (boolean): (False) Compare the A and B topologies from a single input file..

• last_energy_term (string): (None) Last energy term to compare..

• binary_path (string): (gmx) Path to the GROMACS executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (gromacs/gromacs:2022.2) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

JSON

Gmx_cluster

Wrapper of the GROMACS cluster module for clustering structures from a given GROMACS compatible trajectory.

Get help

Command:

gmx_cluster -h

usage: gmx_cluster [-h] [-c CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_traj_path INPUT_TRAJ_PATH [--input_index_path INPUT_INDEX_PATH] --output_pdb_path OUTPUT_PDB_PATH [--output_cluster_log_path OUTPUT_CLUSTER_LOG_PATH] [--output_rmsd_cluster_xpm_path OUTPUT_RMSD_CLUSTER_XPM_PATH] [--output_rmsd_dist_xvg_path OUTPUT_RMSD_DIST_XVG_PATH]

Creates cluster structures from a given GROMACS compatible trajectory.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_structure_path INPUT_STRUCTURE_PATH
                        Path to the input structure file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  --output_pdb_path OUTPUT_PDB_PATH
                        Path to the output cluster file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.

optional arguments:
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.
  --output_cluster_log_path OUTPUT_CLUSTER_LOG_PATH
                        Path to the output log file. Accepted formats: log.
  --output_rmsd_cluster_xpm_path OUTPUT_RMSD_CLUSTER_XPM_PATH
                        Path to the output X PixMap compatible matrix file. Accepted formats: xpm.
  --output_rmsd_dist_xvg_path OUTPUT_RMSD_DIST_XVG_PATH
                        Path to xvgr/xmgr file. Accepted formats: xvg.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_structure_path (string): Path to the input structure file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT

• input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG

• input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX

• output_pdb_path (string): Path to the output cluster file. File type: output. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG

• output_cluster_log_path (string): Path to the output log file. File type: output. Sample file. Accepted formats: LOG

• output_rmsd_cluster_xpm_path (string): Path to the output X PixMap compatible matrix file. File type: output. Sample file. Accepted formats: XPM

• output_rmsd_dist_xvg_path (string): Path to xvgr/xmgr file. File type: output. Sample file. Accepted formats: XVG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• fit_selection (string): (System) Group where the fitting will be performed. If input_index_path provided, check the file for the accepted values. .

• output_selection (string): (System) Group that is going to be written in the output trajectory. If input_index_path provided, check the file for the accepted values. .

• dista (boolean): (False) Use RMSD of distances instead of RMS deviation..

• nofit (boolean): (False) Do not use least squares fitting before RMSD calculation..

• method (string): (linkage) Method for cluster determination. .

• cutoff (number): (0.1) RMSD cut-off (nm) for two structures to be neighbor..

• binary_path (string): (gmx) Path to the GROMACS executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (gromacs/gromacs:2022.2) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  cutoff: 0.1
  dista: false
  fit_selection: System
  method: linkage
  output_selection: System

Docker config file

properties:
  container_image: gromacs/gromacs:2022.2
  container_path: docker
  container_user_id: '1000'
  container_volume_path: /tmp
  cutoff: 0.1
  dista: false
  fit_selection: System
  method: linkage
  output_selection: System

Singularity config file

properties:
  container_image: shub://michael-tn/gromacs
  container_path: singularity
  container_volume_path: /tmp
  cutoff: 0.1
  dista: false
  fit_selection: System
  method: linkage
  output_selection: System

Command line

gmx_cluster --config config_gmx_cluster.yml --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_pdb_path ref_cluster.pdb --output_cluster_log_path gmx_cluster_cluster.log --output_rmsd_cluster_xpm_path gmx_cluster_rmsd-clust.xpm --output_rmsd_dist_xvg_path gmx_cluster_rmsd-dist.xvg

JSON

Common config file

{
  "properties": {
    "fit_selection": "System",
    "output_selection": "System",
    "dista": false,
    "method": "linkage",
    "cutoff": 0.1
  }
}

Docker config file

{
  "properties": {
    "fit_selection": "System",
    "output_selection": "System",
    "dista": false,
    "method": "linkage",
    "cutoff": 0.1,
    "container_path": "docker",
    "container_image": "gromacs/gromacs:2022.2",
    "container_volume_path": "/tmp",
    "container_user_id": "1000"
  }
}

Singularity config file

{
  "properties": {
    "fit_selection": "System",
    "output_selection": "System",
    "dista": false,
    "method": "linkage",
    "cutoff": 0.1,
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}

Command line

gmx_cluster --config config_gmx_cluster.json --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_pdb_path ref_cluster.pdb --output_cluster_log_path gmx_cluster_cluster.log --output_rmsd_cluster_xpm_path gmx_cluster_rmsd-clust.xpm --output_rmsd_dist_xvg_path gmx_cluster_rmsd-dist.xvg

Gmx_energy

Wrapper of the GROMACS energy module for extracting energy components from a given GROMACS energy file.

Get help

Command:

gmx_energy -h

usage: gmx_energy [-h] [-c CONFIG] -i INPUT_ENERGY_PATH -o OUTPUT_XVG_PATH

Extracts energy components from a given GROMACS energy file.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  -i INPUT_ENERGY_PATH, --input_energy_path INPUT_ENERGY_PATH
                        Path to the input EDR file. Accepted formats: edr.
  -o OUTPUT_XVG_PATH, --output_xvg_path OUTPUT_XVG_PATH
                        Path to the XVG output file. Accepted formats: xvg.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_energy_path (string): Path to the input EDR file. File type: input. Sample file. Accepted formats: EDR

• output_xvg_path (string): Path to the XVG output file. File type: output. Sample file. Accepted formats: XVG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• xvg (string): (none) XVG plot formatting. .

• terms (array): ([Potential]) Energy terms. .

• binary_path (string): (gmx) Path to the GROMACS executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (gromacs/gromacs:2022.2) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  terms:
  - Potential
  - Pressure

Docker config file

properties:
  container_image: gromacs/gromacs:2022.2
  container_path: docker
  container_user_id: '1000'
  container_volume_path: /tmp
  terms:
  - Potential
  - Pressure

Singularity config file

properties:
  container_image: shub://michael-tn/gromacs
  container_path: singularity
  container_volume_path: /tmp
  terms:
  - Potential
  - Pressure

Command line

gmx_energy --config config_gmx_energy.yml --input_energy_path energy.edr --output_xvg_path ref_energy.xvg

JSON

Common config file

{
  "properties": {
    "terms": [
      "Potential",
      "Pressure"
    ]
  }
}

Docker config file

{
  "properties": {
    "terms": [
      "Potential",
      "Pressure"
    ],
    "container_path": "docker",
    "container_image": "gromacs/gromacs:2022.2",
    "container_volume_path": "/tmp",
    "container_user_id": "1000"
  }
}

Singularity config file

{
  "properties": {
    "terms": [
      "Potential",
      "Pressure"
    ],
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}

Command line

gmx_energy --config config_gmx_energy.json --input_energy_path energy.edr --output_xvg_path ref_energy.xvg

Gmx_image

Wrapper of the GROMACS trjconv module for correcting periodicity (image) from a given GROMACS compatible trajectory file.

Get help

Command:

gmx_image -h

usage: gmx_image [-h] [-c CONFIG] --input_traj_path INPUT_TRAJ_PATH --input_top_path INPUT_TOP_PATH [--input_index_path INPUT_INDEX_PATH] -o OUTPUT_TRAJ_PATH

Corrects periodicity (image) from a given GROMACS compatible trajectory file.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  --input_top_path INPUT_TOP_PATH
                        Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  -o OUTPUT_TRAJ_PATH, --output_traj_path OUTPUT_TRAJ_PATH
                        Path to the output file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.

optional arguments:
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG

• input_top_path (string): Path to the GROMACS input topology file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT

• input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX

• output_traj_path (string): Path to the output file. File type: output. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• fit_selection (string): (System) Group where the fitting will be performed. If input_index_path provided, check the file for the accepted values. .

• center_selection (string): (System) Group where the trjconv will be performed. If input_index_path provided, check the file for the accepted values. .

• cluster_selection (string): (System) Group assigned to be the cluster, onto which all atoms are wrapped around the box, such that they are closest to the center of mass of the cluster, which is iteratively updated. If input_index_path provided, check the file for the accepted values. .

• output_selection (string): (System) Group that is going to be written in the output trajectory. If input_index_path provided, check the file for the accepted values. .

• pbc (string): (mol) PBC treatment (see help text for full description) . .

• center (boolean): (True) Center atoms in box..

• ur (string): (compact) Unit-cell representation. .

• fit (string): (none) Fit molecule to ref structure in the structure file. .

• binary_path (string): (gmx) Path to the GROMACS executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (gromacs/gromacs:2022.2) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  center: true
  center_selection: System
  fit: rot+trans
  fit_selection: System
  output_selection: System
  pbc: mol
  ur: compact

Docker config file

properties:
  center: true
  center_selection: System
  container_image: gromacs/gromacs:2022.2
  container_path: docker
  container_user_id: '1000'
  container_volume_path: /tmp
  fit: rot+trans
  fit_selection: System
  output_selection: System
  pbc: mol
  ur: compact

Singularity config file

properties:
  center: true
  center_selection: System
  container_image: shub://michael-tn/gromacs
  container_path: singularity
  container_volume_path: /tmp
  fit: rot+trans
  fit_selection: System
  output_selection: System
  pbc: mol
  ur: compact

Command line

gmx_image --config config_gmx_image.yml --input_traj_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_traj_path ref_image.xtc

JSON

Common config file

{
  "properties": {
    "fit_selection": "System",
    "center_selection": "System",
    "output_selection": "System",
    "pbc": "mol",
    "center": true,
    "fit": "rot+trans",
    "ur": "compact"
  }
}

Docker config file

{
  "properties": {
    "fit_selection": "System",
    "center_selection": "System",
    "output_selection": "System",
    "pbc": "mol",
    "center": true,
    "fit": "rot+trans",
    "ur": "compact",
    "container_path": "docker",
    "container_image": "gromacs/gromacs:2022.2",
    "container_volume_path": "/tmp",
    "container_user_id": "1000"
  }
}

Singularity config file

{
  "properties": {
    "fit_selection": "System",
    "center_selection": "System",
    "output_selection": "System",
    "pbc": "mol",
    "center": true,
    "fit": "rot+trans",
    "ur": "compact",
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}

Command line

gmx_image --config config_gmx_image.json --input_traj_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_traj_path ref_image.xtc

Gmx_rgyr

Wrapper of the GROMACS gyrate module for computing the radius of gyration (Rgyr) of a molecule about the x-, y- and z-axes, as a function of time, from a given GROMACS compatible trajectory.

Get help

Command:

gmx_rgyr -h

usage: gmx_rgyr [-h] [-c CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_traj_path INPUT_TRAJ_PATH [--input_index_path INPUT_INDEX_PATH] -o OUTPUT_XVG_PATH

Computes the radius of gyration (Rgyr) of a molecule about the x-, y- and z-axes, as a function of time, from a given GROMACS compatible trajectory.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_structure_path INPUT_STRUCTURE_PATH
                        Path to the input structure file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  -o OUTPUT_XVG_PATH, --output_xvg_path OUTPUT_XVG_PATH
                        Path to the XVG output file. Accepted formats: xvg.

optional arguments:
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_structure_path (string): Path to the input structure file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT

• input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG

• input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX

• output_xvg_path (string): Path to the XVG output file. File type: output. Sample file. Accepted formats: XVG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• xvg (string): (none) XVG plot formatting. .

• selection (string): (System) Group where the rgyr will be performed. If input_index_path provided, check the file for the accepted values. .

• binary_path (string): (gmx) Path to the GROMACS executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (gromacs/gromacs:2022.2) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  selection: System

Docker config file

properties:
  container_image: gromacs/gromacs:2022.2
  container_path: docker
  container_user_id: '1000'
  container_volume_path: /tmp
  selection: System

Singularity config file

properties:
  container_image: shub://michael-tn/gromacs
  container_path: singularity
  container_volume_path: /tmp
  selection: System

Command line

gmx_rgyr --config config_gmx_rgyr.yml --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_xvg_path ref_rgyr.xvg

JSON

Common config file

{
  "properties": {
    "selection": "System"
  }
}

Docker config file

{
  "properties": {
    "selection": "System",
    "container_path": "docker",
    "container_image": "gromacs/gromacs:2022.2",
    "container_volume_path": "/tmp",
    "container_user_id": "1000"
  }
}

Singularity config file

{
  "properties": {
    "selection": "System",
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}

Command line

gmx_rgyr --config config_gmx_rgyr.json --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_xvg_path ref_rgyr.xvg

Gmx_rms

Wrapper of the GROMACS rms module for performing a Root Mean Square deviation (RMSd) analysis from a given GROMACS compatible trajectory.

Get help

Command:

gmx_rms -h

usage: gmx_rms [-h] [-c CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_traj_path INPUT_TRAJ_PATH [--input_index_path INPUT_INDEX_PATH] -o OUTPUT_XVG_PATH

Performs a Root Mean Square deviation (RMSd) analysis from a given GROMACS compatible trajectory.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_structure_path INPUT_STRUCTURE_PATH
                        Path to the input structure file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  -o OUTPUT_XVG_PATH, --output_xvg_path OUTPUT_XVG_PATH
                        Path to the XVG output file. Accepted formats: xvg.

optional arguments:
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_structure_path (string): Path to the input structure file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT

• input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG

• input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX

• output_xvg_path (string): Path to the XVG output file. File type: output. Sample file. Accepted formats: XVG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• xvg (string): (none) XVG plot formatting. .

• selection (string): (System) Group where the rms will be performed. If input_index_path provided, check the file for the accepted values. .

• binary_path (string): (gmx) Path to the GROMACS executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (gromacs/gromacs:2022.2) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  selection: System

Docker config file

properties:
  container_image: gromacs/gromacs:2022.2
  container_path: docker
  container_user_id: '1000'
  container_volume_path: /tmp
  selection: System

Singularity config file

properties:
  container_image: shub://michael-tn/gromacs
  container_path: singularity
  container_volume_path: /tmp
  selection: System

Command line

gmx_rms --config config_gmx_rms.yml --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_xvg_path ref_rms.xvg

JSON

Common config file

{
  "properties": {
    "selection": "System"
  }
}

Docker config file

{
  "properties": {
    "selection": "System",
    "container_path": "docker",
    "container_image": "gromacs/gromacs:2022.2",
    "container_volume_path": "/tmp",
    "container_user_id": "1000"
  }
}

Singularity config file

{
  "properties": {
    "selection": "System",
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}

Command line

gmx_rms --config config_gmx_rms.json --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_xvg_path ref_rms.xvg

Gmx_rmsf

Wrapper of the GROMACS rmsf module for performing a Root Mean Square Fluctuation (RMSF) analysis from a given GROMACS compatible trajectory.

Get help

Command:

gmx_rmsf -h

/bin/sh: 1: gmx_rmsf: not found

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_structure_path (string): Path to the input structure file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT

• input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG

• input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX

• output_xvg_path (string): Path to the XVG output file. File type: output. Sample file. Accepted formats: XVG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• xvg (string): (none) XVG plot formatting. .

• selection (string): (System) Group where the rmsf will be performed. If input_index_path provided, check the file for the accepted values. .

• binary_path (string): (gmx) Path to the GROMACS executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (gromacs/gromacs:2022.2) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  bfactor: false
  bin_width: 0.1
  demean: true
  hist: false
  mass_weighted: false
  nofit: false
  selection: System

Docker config file

properties:
  bfactor: false
  bin_width: 0.1
  container_image: gromacs/gromacs:2022.2
  container_path: docker
  container_user_id: '1000'
  container_volume_path: /tmp
  demean: true
  hist: false
  mass_weighted: false
  nofit: false
  selection: System

Singularity config file

properties:
  bfactor: false
  bin_width: 0.1
  container_image: shub://michael-tn/gromacs
  container_path: singularity
  container_volume_path: /tmp
  demean: true
  hist: false
  mass_weighted: false
  nofit: false
  selection: System

Command line

gmx_rmsf --config config_gmx_rmsf.yml --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_xvg_path ref_rms.xvg

JSON

Common config file

{
  "properties": {
    "selection": "System",
    "demean": true,
    "mass_weighted": false,
    "nofit": false,
    "bfactor": false,
    "bin_width": 0.1,
    "hist": false
  }
}

Docker config file

{
  "properties": {
    "selection": "System",
    "demean": true,
    "mass_weighted": false,
    "nofit": false,
    "bfactor": false,
    "bin_width": 0.1,
    "hist": false,
    "container_path": "docker",
    "container_image": "gromacs/gromacs:2022.2",
    "container_volume_path": "/tmp",
    "container_user_id": "1000"
  }
}

Singularity config file

{
  "properties": {
    "selection": "System",
    "demean": true,
    "mass_weighted": false,
    "nofit": false,
    "bfactor": false,
    "bin_width": 0.1,
    "hist": false,
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}

Command line

gmx_rmsf --config config_gmx_rmsf.json --input_structure_path topology.tpr --input_traj_path trajectory.trr --input_index_path index.ndx --output_xvg_path ref_rms.xvg

Gmx_trjconv_str

Wrapper of the GROMACS trjconv module for converting between GROMACS compatible structure file formats and/or extracting a selection of atoms.

Get help

Command:

gmx_trjconv_str -h

usage: gmx_trjconv_str [-h] [-c CONFIG] --input_structure_path INPUT_STRUCTURE_PATH --input_top_path INPUT_TOP_PATH [--input_index_path INPUT_INDEX_PATH] -o OUTPUT_STR_PATH

Converts between GROMACS compatible structure file formats and/or extracts a selection of atoms.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_structure_path INPUT_STRUCTURE_PATH
                        Path to the input structure file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  --input_top_path INPUT_TOP_PATH
                        Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  -o OUTPUT_STR_PATH, --output_str_path OUTPUT_STR_PATH
                        Path to the output file. Accepted formats: pdb, xtc, trr, cpt, gro, g96, tng.

optional arguments:
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_structure_path (string): Path to the input structure file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG

• input_top_path (string): Path to the GROMACS input topology file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT

• input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX

• output_str_path (string): Path to the output file. File type: output. Sample file. Accepted formats: PDB, XTC, TRR, CPT, GRO, G96, TNG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• selection (string): (System) Group where the trjconv will be performed. If input_index_path provided, check the file for the accepted values. .

• pbc (string): (mol) PBC treatment (see help text for full description) . .

• center (boolean): (True) Center atoms in box..

• ur (string): (compact) Unit-cell representation. .

• fit (string): (none) Fit molecule to ref structure in the structure file. .

• binary_path (string): (gmx) Path to the GROMACS executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (gromacs/gromacs:2022.2) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  selection: System

Docker config file

properties:
  container_image: gromacs/gromacs:2022.2
  container_path: docker
  container_user_id: '1000'
  container_volume_path: /tmp
  selection: System

Singularity config file

properties:
  container_image: shub://michael-tn/gromacs
  container_path: singularity
  container_volume_path: /tmp
  selection: System

Command line

gmx_trjconv_str --config config_gmx_trjconv_str.yml --input_structure_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_str_path ref_trjconv.str.pdb

JSON

Common config file

{
  "properties": {
    "selection": "System"
  }
}

Docker config file

{
  "properties": {
    "selection": "System",
    "container_path": "docker",
    "container_image": "gromacs/gromacs:2022.2",
    "container_volume_path": "/tmp",
    "container_user_id": "1000"
  }
}

Singularity config file

{
  "properties": {
    "selection": "System",
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}

Command line

gmx_trjconv_str --config config_gmx_trjconv_str.json --input_structure_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_str_path ref_trjconv.str.pdb

Gmx_trjconv_str_ens

Wrapper of the GROMACS trjconv module for extracting an ensemble of frames containing a selection of atoms from GROMACS compatible trajectory files.

Get help

Command:

gmx_trjconv_str_ens -h

usage: gmx_trjconv_str_ens [-h] [-c CONFIG] --input_traj_path INPUT_TRAJ_PATH --input_top_path INPUT_TOP_PATH [--input_index_path INPUT_INDEX_PATH] -o OUTPUT_STR_ENS_PATH

Extracts an ensemble of frames containing a selection of atoms from GROMACS compatible trajectory files.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  --input_top_path INPUT_TOP_PATH
                        Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  -o OUTPUT_STR_ENS_PATH, --output_str_ens_path OUTPUT_STR_ENS_PATH
                        Path to the output file. Accepted formats: zip.

optional arguments:
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG

• input_top_path (string): Path to the GROMACS input topology file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT

• input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX

• output_str_ens_path (string): Path to the output file. File type: output. Sample file. Accepted formats: ZIP

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• selection (string): (System) Group where the trjconv will be performed. If input_index_path provided, check the file for the accepted values. .

• skip (integer): (1) Only write every nr-th frame..

• start (integer): (0) Time of first frame to read from trajectory (default unit ps)..

• end (integer): (0) Time of last frame to read from trajectory (default unit ps)..

• dt (integer): (0) Only write frame when t MOD dt = first time (ps)..

• output_name (string): (output) File name for ensemble of output files..

• output_type (string): (pdb) File type for ensemble of output files. .

• binary_path (string): (gmx) Path to the GROMACS executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (gromacs/gromacs:2022.2) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  dt: 1
  end: 10
  output_name: output
  output_type: pdb
  selection: System
  start: 0

Docker config file

properties:
  container_image: gromacs/gromacs:2022.2
  container_path: docker
  container_user_id: '1000'
  container_volume_path: /tmp
  dt: 1
  end: 10
  output_name: output
  output_type: pdb
  selection: System
  start: 0

Singularity config file

properties:
  container_image: shub://michael-tn/gromacs
  container_path: singularity
  container_volume_path: /tmp
  dt: 1
  end: 10
  output_name: output
  output_type: pdb
  selection: System
  start: 0

Command line

gmx_trjconv_str_ens --config config_gmx_trjconv_str_ens.yml --input_traj_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_str_ens_path ref_trjconv.str.ens.zip

JSON

Common config file

{
  "properties": {
    "selection": "System",
    "start": 0,
    "end": 10,
    "dt": 1,
    "output_name": "output",
    "output_type": "pdb"
  }
}

Docker config file

{
  "properties": {
    "selection": "System",
    "start": 0,
    "end": 10,
    "dt": 1,
    "output_name": "output",
    "output_type": "pdb",
    "container_path": "docker",
    "container_image": "gromacs/gromacs:2022.2",
    "container_volume_path": "/tmp",
    "container_user_id": "1000"
  }
}

Singularity config file

{
  "properties": {
    "selection": "System",
    "start": 0,
    "end": 10,
    "dt": 1,
    "output_name": "output",
    "output_type": "pdb",
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}

Command line

gmx_trjconv_str_ens --config config_gmx_trjconv_str_ens.json --input_traj_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_str_ens_path ref_trjconv.str.ens.zip

Gmx_trjconv_trj

Wrapper of the GROMACS trjconv module for converting between GROMACS compatible trajectory file formats and/or extracts a selection of atoms.

Get help

Command:

gmx_trjconv_trj -h

usage: gmx_trjconv_trj [-h] [-c CONFIG] --input_traj_path INPUT_TRAJ_PATH [--input_top_path INPUT_TOP_PATH] [--input_index_path INPUT_INDEX_PATH] -o OUTPUT_TRAJ_PATH

Converts between GROMACS compatible trajectory file formats and/or extracts a selection of atoms.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        This file can be a YAML file, JSON file or JSON string

required arguments:
  --input_traj_path INPUT_TRAJ_PATH
                        Path to the GROMACS trajectory file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.
  -o OUTPUT_TRAJ_PATH, --output_traj_path OUTPUT_TRAJ_PATH
                        Path to the output file. Accepted formats: xtc, trr, cpt, gro, g96, pdb, tng.

optional arguments:
  --input_top_path INPUT_TOP_PATH
                        Path to the GROMACS input topology file. Accepted formats: tpr, gro, g96, pdb, brk, ent.
  --input_index_path INPUT_INDEX_PATH
                        Path to the GROMACS index file. Accepted formats: ndx.

I / O Arguments

Syntax: input_argument (datatype) : Definition

Config input / output arguments for this building block:

• input_traj_path (string): Path to the GROMACS trajectory file. File type: input. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG

• input_top_path (string): Path to the GROMACS input topology file. File type: input. Sample file. Accepted formats: TPR, GRO, G96, PDB, BRK, ENT

• input_index_path (string): Path to the GROMACS index file. File type: input. Sample file. Accepted formats: NDX

• output_traj_path (string): Path to the output file. File type: output. Sample file. Accepted formats: XTC, TRR, CPT, GRO, G96, PDB, TNG

Config

Syntax: input_parameter (datatype) - (default_value) Definition

Config parameters for this building block:

• selection (string): (System) Group where the trjconv will be performed. If input_index_path provided, check the file for the accepted values. .

• start (integer): (0) Time of first frame to read from trajectory (default unit ps)..

• end (integer): (0) Time of last frame to read from trajectory (default unit ps)..

• dt (integer): (0) Only write frame when t MOD dt = first time (ps)..

• binary_path (string): (gmx) Path to the GROMACS executable binary..

• remove_tmp (boolean): (True) Remove temporal files..

• restart (boolean): (False) Do not execute if output files exist..

• sandbox_path (string): (./) Parent path to the sandbox directory..

• container_path (string): (None) Container path definition..

• container_image (string): (gromacs/gromacs:2022.2) Container image definition..

• container_volume_path (string): (/tmp) Container volume path definition..

• container_working_dir (string): (None) Container working directory definition..

• container_user_id (string): (None) Container user_id definition..

• container_shell_path (string): (/bin/bash) Path to default shell inside the container..

YAML

Common config file

properties:
  dt: 0
  end: 0
  selection: System
  start: 0

Docker config file

properties:
  container_image: gromacs/gromacs:2022.2
  container_path: docker
  container_user_id: '1000'
  container_volume_path: /tmp
  dt: 0
  end: 0
  selection: System
  start: 0

Singularity config file

properties:
  container_image: shub://michael-tn/gromacs
  container_path: singularity
  container_volume_path: /tmp
  dt: 0
  end: 0
  selection: System
  start: 0

Command line

gmx_trjconv_trj --config config_gmx_trjconv_trj.yml --input_traj_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_traj_path ref_trjconv.trj.xtc

JSON

Common config file

{
  "properties": {
    "selection": "System",
    "start": 0,
    "end": 0,
    "dt": 0
  }
}

Docker config file

{
  "properties": {
    "selection": "System",
    "start": 0,
    "end": 0,
    "dt": 0,
    "container_path": "docker",
    "container_image": "gromacs/gromacs:2022.2",
    "container_volume_path": "/tmp",
    "container_user_id": "1000"
  }
}

Singularity config file

{
  "properties": {
    "selection": "System",
    "start": 0,
    "end": 0,
    "dt": 0,
    "container_path": "singularity",
    "container_image": "shub://michael-tn/gromacs",
    "container_volume_path": "/tmp"
  }
}

Command line

gmx_trjconv_trj --config config_gmx_trjconv_trj.json --input_traj_path trajectory.trr --input_top_path topology.tpr --input_index_path index.ndx --output_traj_path ref_trjconv.trj.xtc