BioBB GROMACS Command Line Help
Generic usage:
biobb_command [-h] --config CONFIG --input_file(s) <input_file(s)> --output_file <output_file>
Append_ligand
This class takes a ligand ITP file and inserts it in a topology.
Get help
Command:
append_ligand -h
usage: append_ligand [-h] [-c CONFIG] --input_top_zip_path INPUT_TOP_ZIP_PATH --input_itp_path INPUT_ITP_PATH -o OUTPUT_TOP_ZIP_PATH [--input_posres_itp_path INPUT_POSRES_ITP_PATH]
This command takes a ligand ITP file and inserts it in a topology
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_zip_path INPUT_TOP_ZIP_PATH
Path the input topology TOP and ITP files zipball. Accepted formats: zip.
--input_itp_path INPUT_ITP_PATH
Path to the ligand ITP file to be inserted in the topology. Accepted formats: itp.
-o OUTPUT_TOP_ZIP_PATH, --output_top_zip_path OUTPUT_TOP_ZIP_PATH
Path/Name the output topology TOP and ITP files zipball. Accepted formats: zip.
optional arguments:
--input_posres_itp_path INPUT_POSRES_ITP_PATH
Path to the position restriction ITP file. Accepted formats: itp.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_top_zip_path (string): Path the input topology TOP and ITP files zipball. File type: input. Sample file. Accepted formats: ZIP
input_itp_path (string): Path to the ligand ITP file to be inserted in the topology. File type: input. Sample file. Accepted formats: ITP
output_top_zip_path (string): Path/Name the output topology TOP and ITP files zipball. File type: output. Sample file. Accepted formats: ZIP
input_posres_itp_path (string): Path to the position restriction ITP file. File type: input. Sample file. Accepted formats: ITP
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
posres_name (string): (POSRES_LIGAND) String to be included in the ifdef clause.
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.
YAML
Common config file
properties:
posres_name: POSRES_LIGAND
Command line
append_ligand --config config_append_ligand.yml --input_top_zip_path ndx2resttop.zip --input_itp_path pep_ligand.itp --output_top_zip_path ref_appendligand.zip --input_posres_itp_path input.itp
JSON
Common config file
{
"properties": {
"posres_name": "POSRES_LIGAND"
}
}
Command line
append_ligand --config config_append_ligand.json --input_top_zip_path ndx2resttop.zip --input_itp_path pep_ligand.itp --output_top_zip_path ref_appendligand.zip --input_posres_itp_path input.itp
Convert_tpr
Wrapper of the GROMACS convert-tpr module.
Get help
Command:
convert_tpr -h
usage: convert_tpr [-h] [-c CONFIG] --input_tpr_path INPUT_TPR_PATH -o OUTPUT_TPR_PATH [--input_ndx_path INPUT_NDX_PATH]
Wrapper of the GROMACS convert-tpr module.
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_tpr_path INPUT_TPR_PATH
Path to the input portable binary run file TPR. Accepted formats: tpr.
-o OUTPUT_TPR_PATH, --output_tpr_path OUTPUT_TPR_PATH
Path to the output portable binary run file TPR. Accepted formats: tpr.
optional arguments:
--input_ndx_path INPUT_NDX_PATH
Path to the input index NDX file, used to trim the tpr file to a subset of atoms. Accepted formats: ndx.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_tpr_path (string): Path to the input portable binary run file TPR. File type: input. Sample file. Accepted formats: TPR
output_tpr_path (string): Path to the output portable binary run file TPR. File type: output. Sample file. Accepted formats: TPR
input_ndx_path (string): Path to the input index NDX file, used to trim the tpr file to a subset of atoms. File type: input. Sample file. Accepted formats: NDX
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
extend (integer): (0) Extend the runtime by this amount (ps).
until (integer): (0) Extend the runtime until this ending time (ps).
nsteps (integer): (0) Change the number of steps remaining to be made.
output_group (string): (System) Index group to write to the output tpr file when trimming to a subset of atoms. Only used when input_ndx_path is provided.
gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable.
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) Path to the binary executable of your container.
container_image (string): (gromacs/gromacs:latest) Container Image identifier.
container_volume_path (string): (/data) Path to an internal directory in the container.
container_working_dir (string): (None) Path to the internal CWD in the container.
container_user_id (string): (None) User number id to be mapped inside the container.
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell.
YAML
Common config file
properties:
nsteps: 100
Docker config file
properties:
container_image: quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp
nsteps: 100
Singularity config file
properties:
container_image: https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: singularity
container_volume_path: /tmp
container_working_dir: /tmp
nsteps: 100
Command line
convert_tpr --config config_convert_tpr.yml --input_tpr_path ref_grompp.tpr --output_tpr_path ref_grompp.tpr --input_ndx_path input.ndx
JSON
Common config file
{
"properties": {
"nsteps": 100
}
}
Docker config file
{
"properties": {
"nsteps": 100,
"container_path": "docker",
"container_image": "quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Singularity config file
{
"properties": {
"nsteps": 100,
"container_path": "singularity",
"container_image": "https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
convert_tpr --config config_convert_tpr.json --input_tpr_path ref_grompp.tpr --output_tpr_path ref_grompp.tpr --input_ndx_path input.ndx
Editconf
Wrapper class for the GROMACS editconf module.
Get help
Command:
editconf -h
usage: editconf [-h] [-c CONFIG] -i INPUT_GRO_PATH -o OUTPUT_GRO_PATH
Wrapper of the GROMACS gmx editconf module.
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_GRO_PATH, --input_gro_path INPUT_GRO_PATH
Path to the input GRO file. Accepted formats: gro, pdb.
-o OUTPUT_GRO_PATH, --output_gro_path OUTPUT_GRO_PATH
Path to the output GRO file. Accepted formats: pdb, gro.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_gro_path (string): Path to the input GRO file. File type: input. Sample file. Accepted formats: GRO, PDB
output_gro_path (string): Path to the output GRO file. File type: output. Sample file. Accepted formats: PDB, GRO
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
distance_to_molecule (number): (1.0) Distance of the box from the outermost atom in nm. ie 1.0nm = 10 Angstroms.
box_vector_lenghts (string): (None) Array of floats defining the box vector lenghts ie “0.5 0.5 0.5”. If this option is used the distance_to_molecule property will be ignored.
box_type (string): (cubic) Geometrical shape of the solvent box.
center_molecule (boolean): (True) Center molecule in the box.
gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable.
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) Path to the binary executable of your container.
container_image (string): (None) Container Image identifier.
container_volume_path (string): (/data) Path to an internal directory in the container.
container_working_dir (string): (None) Path to the internal CWD in the container.
container_user_id (string): (None) User number id to be mapped inside the container.
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell.
YAML
Common config file
properties:
box_type: cubic
distance_to_molecule: 1.0
Docker config file
properties:
box_type: cubic
container_image: quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp
distance_to_molecule: 1.0
Singularity config file
properties:
box_type: cubic
container_image: https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: singularity
container_volume_path: /tmp
container_working_dir: /tmp
distance_to_molecule: 1.0
Command line
editconf --config config_editconf.yml --input_gro_path editconf.gro --output_gro_path ref_editconf.gro
JSON
Common config file
{
"properties": {
"distance_to_molecule": 1.0,
"box_type": "cubic"
}
}
Docker config file
{
"properties": {
"distance_to_molecule": 1.0,
"box_type": "cubic",
"container_path": "docker",
"container_image": "quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Singularity config file
{
"properties": {
"distance_to_molecule": 1.0,
"box_type": "cubic",
"container_path": "singularity",
"container_image": "https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
editconf --config config_editconf.json --input_gro_path editconf.gro --output_gro_path ref_editconf.gro
Genion
Wrapper class for the GROMACS genion module.
Get help
Command:
genion -h
usage: genion [-h] [-c CONFIG] --input_tpr_path INPUT_TPR_PATH --output_gro_path OUTPUT_GRO_PATH --input_top_zip_path INPUT_TOP_ZIP_PATH --output_top_zip_path OUTPUT_TOP_ZIP_PATH [--input_ndx_path INPUT_NDX_PATH]
Wrapper for the GROMACS genion module.
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_tpr_path INPUT_TPR_PATH
Path to the input portable run input TPR file. Accepted formats: tpr.
--output_gro_path OUTPUT_GRO_PATH
Path to the input structure GRO file. Accepted formats: gro.
--input_top_zip_path INPUT_TOP_ZIP_PATH
Path the input TOP topology in zip format. Accepted formats: zip.
--output_top_zip_path OUTPUT_TOP_ZIP_PATH
Path the output topology TOP and ITP files zipball. Accepted formats: zip.
optional arguments:
--input_ndx_path INPUT_NDX_PATH
Path to the input index NDX file. Accepted formats: ndx.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_tpr_path (string): Path to the input portable run input TPR file. File type: input. Sample file. Accepted formats: TPR
output_gro_path (string): Path to the input structure GRO file. File type: output. Sample file. Accepted formats: GRO
input_top_zip_path (string): Path the input TOP topology in zip format. File type: input. Sample file. Accepted formats: ZIP
output_top_zip_path (string): Path the output topology TOP and ITP files zipball. File type: output. Sample file. Accepted formats: ZIP
input_ndx_path (string): Path to the input index NDX file. File type: input. Sample file. Accepted formats: NDX
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
replaced_group (string): (SOL) Group of molecules that will be replaced by the solvent.
neutral (boolean): (False) Neutralize the charge of the system.
pname (string): (NA) Name of the positive ion.
nname (string): (CL) Name of the negative ion.
np (integer): (0) Number of positive ions to add.
nn (integer): (0) Number of negative ions to add.
pq (integer): (1) Charge of the positive ion.
nq (integer): (-1) Charge of the negative ion.
rmin (number): (0.6) Minimum distance between ions and non-solvent in nm.
concentration (number): (0.0) Concentration of the ions in (mol/liter). When nonzero, overrides np and nn. Neutralization adds ions on top of the specified counts or concentration.
seed (integer): (1993) Seed for random number generator.
gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable.
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) Path to the binary executable of your container.
container_image (string): (gromacs/gromacs:latest) Container Image identifier.
container_volume_path (string): (/data) Path to an internal directory in the container.
container_working_dir (string): (None) Path to the internal CWD in the container.
container_user_id (string): (None) User number id to be mapped inside the container.
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell.
YAML
Common config file
properties:
concentration: 0.05
replaced_group: SOL
Docker config file
properties:
concentration: 0.05
container_image: quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp
replaced_group: SOL
Singularity config file
properties:
concentration: 0.05
container_image: https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: singularity
container_volume_path: /tmp
container_working_dir: /tmp
replaced_group: SOL
Command line
genion --config config_genion.yml --input_tpr_path genion.tpr --output_gro_path ref_genion.gro --input_top_zip_path genion.zip --output_top_zip_path ref_genion.zip --input_ndx_path input.ndx
JSON
Common config file
{
"properties": {
"concentration": 0.05,
"replaced_group": "SOL"
}
}
Docker config file
{
"properties": {
"concentration": 0.05,
"replaced_group": "SOL",
"container_path": "docker",
"container_image": "quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Singularity config file
{
"properties": {
"concentration": 0.05,
"replaced_group": "SOL",
"container_path": "singularity",
"container_image": "https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
genion --config config_genion.json --input_tpr_path genion.tpr --output_gro_path ref_genion.gro --input_top_zip_path genion.zip --output_top_zip_path ref_genion.zip --input_ndx_path input.ndx
Genrestr
Wrapper of the GROMACS genrestr module.
Get help
Command:
genrestr -h
usage: genrestr [-h] [-c CONFIG] --input_structure_path INPUT_STRUCTURE_PATH -o OUTPUT_ITP_PATH [--input_ndx_path INPUT_NDX_PATH]
Wrapper for the GROMACS genrestr module.
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 PDB, GRO or TPR format. Accepted formats: pdb, gro, tpr.
-o OUTPUT_ITP_PATH, --output_itp_path OUTPUT_ITP_PATH
Path the output ITP topology file with restrains. Accepted formats: itp.
optional arguments:
--input_ndx_path INPUT_NDX_PATH
Path to the input GROMACS index file, NDX format. 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 PDB, GRO or TPR format. File type: input. Sample file. Accepted formats: PDB, GRO, TPR
output_itp_path (string): Path the output ITP topology file with restrains. File type: output. Sample file. Accepted formats: ITP
input_ndx_path (string): Path to the input GROMACS index file, NDX format. File type: input. Sample file. Accepted formats: NDX
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
restrained_group (string): (system) Index group that will be restrained.
force_constants (string): (500 500 500) Array of three floats defining the force constants
gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable.
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) Path to the binary executable of your container.
container_image (string): (gromacs/gromacs:latest) Container Image identifier.
container_volume_path (string): (/data) Path to an internal directory in the container.
container_working_dir (string): (None) Path to the internal CWD in the container.
container_user_id (string): (None) User number id to be mapped inside the container.
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell.
YAML
Common config file
properties:
force_constants: 500 500 500
restrained_group: system
Docker config file
properties:
container_image: quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp
force_constants: 500 500 500
restrained_group: system
Singularity config file
properties:
container_image: https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: singularity
container_volume_path: /tmp
container_working_dir: /tmp
force_constants: 500 500 500
restrained_group: system
Command line
genrestr --config config_genrestr.yml --input_structure_path genrestr.gro --output_itp_path ref_genrestr.itp --input_ndx_path genrestr.ndx
JSON
Common config file
{
"properties": {
"restrained_group": "system",
"force_constants": "500 500 500"
}
}
Docker config file
{
"properties": {
"restrained_group": "system",
"force_constants": "500 500 500",
"container_path": "docker",
"container_image": "quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Singularity config file
{
"properties": {
"restrained_group": "system",
"force_constants": "500 500 500",
"container_path": "singularity",
"container_image": "https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
genrestr --config config_genrestr.json --input_structure_path genrestr.gro --output_itp_path ref_genrestr.itp --input_ndx_path genrestr.ndx
Gmxselect
Wrapper of the GROMACS select module.
Get help
Command:
gmxselect -h
usage: gmxselect [-h] [-c CONFIG] --input_structure_path INPUT_STRUCTURE_PATH -o OUTPUT_NDX_PATH [--input_ndx_path INPUT_NDX_PATH]
Wrapper for the GROMACS select module.
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 GRO/PDB/TPR file. Accepted formats: pdb, gro, tpr.
-o OUTPUT_NDX_PATH, --output_ndx_path OUTPUT_NDX_PATH
Path to the output index NDX file. Accepted formats: ndx.
optional arguments:
--input_ndx_path INPUT_NDX_PATH
Path to the input index NDX 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 GRO/PDB/TPR file. File type: input. Sample file. Accepted formats: PDB, GRO, TPR
output_ndx_path (string): Path to the output index NDX file. File type: output. Sample file. Accepted formats: NDX
input_ndx_path (string): Path to the input index NDX file. File type: input. Sample file. Accepted formats: NDX
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
selection (string): (a CA C N O) Heavy atoms. Atom selection string.
append (boolean): (False) Append the content of the input_ndx_path to the output_ndx_path.
binary_path (string): (gmx) Path to the GROMACS executable binary.
gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable.
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) Path to the binary executable of your container.
container_image (string): (gromacs/gromacs:latest) Container Image identifier.
container_volume_path (string): (/data) Path to an internal directory in the container.
container_working_dir (string): (None) Path to the internal CWD in the container.
container_user_id (string): (None) User number id to be mapped inside the container.
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell.
YAML
Common config file
properties:
selection: '"Mynewgroup" group "Protein-H" and not same residue as within 0.4 of
resname ARG'
Docker config file
properties:
container_image: quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp
selection: '"Mynewgroup" group "Protein-H" and not same residue as within 0.4 of
resname ARG'
Singularity config file
properties:
container_image: https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: singularity
container_volume_path: /tmp
container_working_dir: /tmp
selection: '"Mynewgroup" group "Protein-H" and not same residue as within 0.4 of
resname ARG'
Command line
gmxselect --config config_gmxselect.yml --input_structure_path make_ndx.tpr --output_ndx_path ref_select.ndx --input_ndx_path input.ndx
JSON
Common config file
{
"properties": {
"selection": "\"Mynewgroup\" group \"Protein-H\" and not same residue as within 0.4 of resname ARG"
}
}
Docker config file
{
"properties": {
"selection": "\"Mynewgroup\" group \"Protein-H\" and not same residue as within 0.4 of resname ARG",
"container_path": "docker",
"container_image": "quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Singularity config file
{
"properties": {
"selection": "\"Mynewgroup\" group \"Protein-H\" and not same residue as within 0.4 of resname ARG",
"container_path": "singularity",
"container_image": "https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
gmxselect --config config_gmxselect.json --input_structure_path make_ndx.tpr --output_ndx_path ref_select.ndx --input_ndx_path input.ndx
Grompp
Wrapper of the GROMACS grompp module.
Get help
Command:
grompp -h
usage: grompp [-h] [-c CONFIG] --input_gro_path INPUT_GRO_PATH --input_top_zip_path INPUT_TOP_ZIP_PATH -o OUTPUT_TPR_PATH [--input_cpt_path INPUT_CPT_PATH] [--input_ndx_path INPUT_NDX_PATH] [--input_mdp_path INPUT_MDP_PATH]
Wrapper for the GROMACS grompp module.
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_gro_path INPUT_GRO_PATH
Path to the input GROMACS structure GRO file. Accepted formats: gro.
--input_top_zip_path INPUT_TOP_ZIP_PATH
Path to the input GROMACS topology TOP and ITP files in zip format. Accepted formats: zip.
-o OUTPUT_TPR_PATH, --output_tpr_path OUTPUT_TPR_PATH
Path to the output portable binary run file TPR. Accepted formats: tpr.
optional arguments:
--input_cpt_path INPUT_CPT_PATH
Path to the input GROMACS checkpoint file CPT. Accepted formats: cpt.
--input_ndx_path INPUT_NDX_PATH
Path to the input GROMACS index files NDX. Accepted formats: ndx.
--input_mdp_path INPUT_MDP_PATH
Path to the input GROMACS `MDP file <http://manual.gromacs.org/current/user-guide/mdp-options.html>`_. Accepted formats: mdp.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_gro_path (string): Path to the input GROMACS structure GRO file. File type: input. Sample file. Accepted formats: GRO
input_top_zip_path (string): Path to the input GROMACS topology TOP and ITP files in zip format. File type: input. Sample file. Accepted formats: ZIP
output_tpr_path (string): Path to the output portable binary run file TPR. File type: output. Sample file. Accepted formats: TPR
input_cpt_path (string): Path to the input GROMACS checkpoint file CPT. File type: input. Sample file. Accepted formats: CPT
input_ndx_path (string): Path to the input GROMACS index files NDX. File type: input. Sample file. Accepted formats: NDX
input_mdp_path (string): Path to the input GROMACS MDP file. File type: input. Sample file. Accepted formats: MDP
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
mdp (object): ({}) MDP options specification.
simulation_type (string): (None) Default options for the mdp file. Each one creates a different mdp file.
maxwarn (integer): (0) Maximum number of allowed warnings. If simulation_type is index default is 10.
gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable.
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) Path to the binary executable of your container.
container_image (string): (gromacs/gromacs:latest) Container Image identifier.
container_volume_path (string): (/data) Path to an internal directory in the container.
container_working_dir (string): (None) Path to the internal CWD in the container.
container_user_id (string): (None) User number id to be mapped inside the container.
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell.
YAML
Common config file
properties:
maxwarn: 1
mdp:
ld-seed: '1'
Docker config file
properties:
container_image: quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp
maxwarn: 1
mdp:
ld-seed: '1'
Singularity config file
properties:
container_image: https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: singularity
container_volume_path: /tmp
container_working_dir: /tmp
maxwarn: 1
mdp:
ld-seed: '1'
Command line
grompp --config config_grompp.yml --input_gro_path grompp.gro --input_top_zip_path grompp.zip --output_tpr_path ref_grompp.tpr --input_cpt_path input.cpt --input_ndx_path input.ndx --input_mdp_path input.mdp
JSON
Common config file
{
"properties": {
"maxwarn": 1,
"mdp": {
"ld-seed": "1"
}
}
}
Docker config file
{
"properties": {
"maxwarn": 1,
"mdp": {
"ld-seed": "1"
},
"container_path": "docker",
"container_image": "quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Singularity config file
{
"properties": {
"maxwarn": 1,
"mdp": {
"ld-seed": "1"
},
"container_path": "singularity",
"container_image": "https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
grompp --config config_grompp.json --input_gro_path grompp.gro --input_top_zip_path grompp.zip --output_tpr_path ref_grompp.tpr --input_cpt_path input.cpt --input_ndx_path input.ndx --input_mdp_path input.mdp
Grompp_mdrun
Wrapper of the GROMACS grompp module and the GROMACS mdrun module.
Get help
Command:
grompp_mdrun -h
usage: grompp_mdrun [-h] [-c CONFIG] --input_gro_path INPUT_GRO_PATH --input_top_zip_path INPUT_TOP_ZIP_PATH --output_trr_path OUTPUT_TRR_PATH --output_gro_path OUTPUT_GRO_PATH --output_edr_path OUTPUT_EDR_PATH --output_log_path OUTPUT_LOG_PATH [--input_cpt_path INPUT_CPT_PATH] [--input_ndx_path INPUT_NDX_PATH] [--input_mdp_path INPUT_MDP_PATH] [--output_xtc_path OUTPUT_XTC_PATH] [--output_cpt_path OUTPUT_CPT_PATH] [--output_dhdl_path OUTPUT_DHDL_PATH]
Wrapper for the GROMACS grompp_mdrun module.
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_gro_path INPUT_GRO_PATH
Path to the input GROMACS structure GRO file. Accepted formats: gro.
--input_top_zip_path INPUT_TOP_ZIP_PATH
Path to the input GROMACS topology TOP and ITP files in zip format. Accepted formats: zip.
--output_trr_path OUTPUT_TRR_PATH
Path to the GROMACS uncompressed raw trajectory file TRR. Accepted formats: trr.
--output_gro_path OUTPUT_GRO_PATH
Path to the output GROMACS structure GRO file. Accepted formats: gro.
--output_edr_path OUTPUT_EDR_PATH
Path to the output GROMACS portable energy file EDR. Accepted formats: edr.
--output_log_path OUTPUT_LOG_PATH
Path to the output GROMACS trajectory log file LOG. Accepted formats: log.
optional arguments:
--input_cpt_path INPUT_CPT_PATH
Path to the input GROMACS checkpoint file CPT. Accepted formats: cpt.
--input_ndx_path INPUT_NDX_PATH
Path to the input GROMACS index files NDX. Accepted formats: ndx.
--input_mdp_path INPUT_MDP_PATH
Path to the input GROMACS `MDP file <http://manual.gromacs.org/current/user-guide/mdp-options.html>`_. Accepted formats: mdp.
--output_xtc_path OUTPUT_XTC_PATH
Path to the GROMACS compressed trajectory file XTC. Accepted formats: xtc.
--output_cpt_path OUTPUT_CPT_PATH
Path to the output GROMACS checkpoint file CPT. Accepted formats: cpt.
--output_dhdl_path OUTPUT_DHDL_PATH
Path to the output dhdl.xvg file only used when free energy calculation is turned on. Accepted formats: xvg.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_gro_path (string): Path to the input GROMACS structure GRO file. File type: input. Sample file. Accepted formats: GRO
input_top_zip_path (string): Path to the input GROMACS topology TOP and ITP files in zip format. File type: input. Sample file. Accepted formats: ZIP
output_trr_path (string): Path to the GROMACS uncompressed raw trajectory file TRR. File type: output. Sample file. Accepted formats: TRR
output_gro_path (string): Path to the output GROMACS structure GRO file. File type: output. Sample file. Accepted formats: GRO
output_edr_path (string): Path to the output GROMACS portable energy file EDR. File type: output. Sample file. Accepted formats: EDR
output_log_path (string): Path to the output GROMACS trajectory log file LOG. File type: output. Sample file. Accepted formats: LOG
input_cpt_path (string): Path to the input GROMACS checkpoint file CPT. File type: input. Sample file. Accepted formats: CPT
input_ndx_path (string): Path to the input GROMACS index files NDX. File type: input. Sample file. Accepted formats: NDX
input_mdp_path (string): Path to the input GROMACS MDP file. File type: input. Sample file. Accepted formats: MDP
output_xtc_path (string): Path to the GROMACS compressed trajectory file XTC. File type: output. Sample file. Accepted formats: XTC
output_cpt_path (string): Path to the output GROMACS checkpoint file CPT. File type: output. Sample file. Accepted formats: CPT
output_dhdl_path (string): Path to the output dhdl.xvg file only used when free energy calculation is turned on. File type: output. Sample file. Accepted formats: XVG
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
mdp (object): ({}) MDP options specification.
simulation_type (string): (minimization) Default options for the mdp file. Each creates a different mdp file.
maxwarn (integer): (10) Maximum number of allowed warnings.
mpi_bin (string): (None) Path to the MPI runner. Usually “mpirun” or “srun”.
mpi_np (string): (None) Number of MPI processes. Usually an integer bigger than 1.
mpi_hostlist (string): (None) Path to the MPI hostlist file.
checkpoint_time (integer): (15) Checkpoint writing interval in minutes. Only enabled if an output_cpt_path is provided.
num_threads (integer): (0) Let GROMACS guess. The number of threads that are going to be used.
num_threads_mpi (integer): (0) Let GROMACS guess. The number of GROMACS MPI threads that are going to be used.
num_threads_omp (integer): (0) Let GROMACS guess. The number of GROMACS OPENMP threads that are going to be used.
num_threads_omp_pme (integer): (0) Let GROMACS guess. The number of GROMACS OPENMP_PME threads that are going to be used.
use_gpu (boolean): (False) Use settings appropriate for GPU. Adds: -nb gpu -pme gpu
gpu_id (string): (None) list of unique GPU device IDs available to use.
gpu_tasks (string): (None) list of GPU device IDs, mapping each PP task on each node to a device.
gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable.
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) Path to the binary executable of your container.
container_image (string): (gromacs/gromacs:latest) Container Image identifier.
container_volume_path (string): (/data) Path to an internal directory in the container.
container_working_dir (string): (None) Path to the internal CWD in the container.
container_user_id (string): (None) User number id to be mapped inside the container.
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell.
YAML
Common config file
properties:
binary_path: gmx
maxwarn: 1
mdp:
dt: 0.0001
ld-seed: '1'
num_threads: 0
simulation_type: free
Docker config file
properties:
binary_path: gmx
container_image: quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp
maxwarn: 1
mdp:
dt: 0.0001
ld-seed: '1'
num_threads: 0
simulation_type: free
Singularity config file
properties:
binary_path: gmx
container_image: https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: singularity
container_volume_path: /tmp
container_working_dir: /tmp
mdp:
dt: 0.0001
ld-seed: '1'
num_threads: 0
simulation_type: free
Command line
grompp_mdrun --config config_grompp_mdrun.yml --input_gro_path grompp.gro --input_top_zip_path grompp.zip --output_trr_path ref_mdrun.trr --output_gro_path ref_mdrun.gro --output_edr_path ref_mdrun.edr --output_log_path ref_gmx_mdrun.log --input_cpt_path input.cpt --input_ndx_path input.ndx --input_mdp_path input.mdp --output_xtc_path output.xtc --output_cpt_path output.cpt --output_dhdl_path output.xvg
JSON
Common config file
{
"properties": {
"simulation_type": "free",
"maxwarn": 1,
"mdp": {
"ld-seed": "1",
"dt": 0.0001
},
"num_threads": 0,
"binary_path": "gmx"
}
}
Docker config file
{
"properties": {
"simulation_type": "free",
"maxwarn": 1,
"mdp": {
"ld-seed": "1",
"dt": 0.0001
},
"num_threads": 0,
"binary_path": "gmx",
"container_path": "docker",
"container_image": "quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Singularity config file
{
"properties": {
"simulation_type": "free",
"mdp": {
"ld-seed": "1",
"dt": 0.0001
},
"num_threads": 0,
"binary_path": "gmx",
"container_path": "singularity",
"container_image": "https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
grompp_mdrun --config config_grompp_mdrun.json --input_gro_path grompp.gro --input_top_zip_path grompp.zip --output_trr_path ref_mdrun.trr --output_gro_path ref_mdrun.gro --output_edr_path ref_mdrun.edr --output_log_path ref_gmx_mdrun.log --input_cpt_path input.cpt --input_ndx_path input.ndx --input_mdp_path input.mdp --output_xtc_path output.xtc --output_cpt_path output.cpt --output_dhdl_path output.xvg
Make_ndx
Wrapper of the GROMACS make_ndx module.
Get help
Command:
make_ndx -h
usage: make_ndx [-h] [-c CONFIG] --input_structure_path INPUT_STRUCTURE_PATH -o OUTPUT_NDX_PATH [--input_ndx_path INPUT_NDX_PATH]
Wrapper for the GROMACS make_ndx module.
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 GRO/PDB/TPR file. Accepted formats: gro, pdb, tpr.
-o OUTPUT_NDX_PATH, --output_ndx_path OUTPUT_NDX_PATH
Path to the output index NDX file. Accepted formats: ndx.
optional arguments:
--input_ndx_path INPUT_NDX_PATH
Path to the input index NDX 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 GRO/PDB/TPR file. File type: input. Sample file. Accepted formats: GRO, PDB, TPR
output_ndx_path (string): Path to the output index NDX file. File type: output. Sample file. Accepted formats: NDX
input_ndx_path (string): Path to the input index NDX file. File type: input. Sample file. Accepted formats: NDX
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
selection (string): (a CA C N O) Heavy atoms. Atom selection string.
gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable.
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) Path to the binary executable of your container.
container_image (string): (gromacs/gromacs:latest) Container Image identifier.
container_volume_path (string): (/data) Path to an internal directory in the container.
container_working_dir (string): (None) Path to the internal CWD in the container.
container_user_id (string): (None) User number id to be mapped inside the container.
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell.
YAML
Common config file
properties:
selection: 'a C*
0 & ! 13
name 14 FREEZE'
Docker config file
properties:
container_image: quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp21.4
selection: 'a C*
0 & ! 13
name 14 FREEZE'
Singularity config file
properties:
container_image: https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: singularity
container_volume_path: /tmp
container_working_dir: /tmp
selection: 'a C*
0 & ! 13
name 14 FREEZE'
Command line
make_ndx --config config_make_ndx.yml --input_structure_path make_ndx.tpr --output_ndx_path ref_make_ndx.ndx --input_ndx_path input.ndx
JSON
Common config file
{
"properties": {
"selection": "a C*\n0 & ! 13\nname 14 FREEZE"
}
}
Docker config file
{
"properties": {
"selection": "a C*\n0 & ! 13\nname 14 FREEZE",
"container_path": "docker",
"container_image": "quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp21.4"
}
}
Singularity config file
{
"properties": {
"selection": "a C*\n0 & ! 13\nname 14 FREEZE",
"container_path": "singularity",
"container_image": "https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
make_ndx --config config_make_ndx.json --input_structure_path make_ndx.tpr --output_ndx_path ref_make_ndx.ndx --input_ndx_path input.ndx
Mdrun
Wrapper of the GROMACS mdrun module.
Get help
Command:
mdrun -h
usage: mdrun [-h] [-c CONFIG] --input_tpr_path INPUT_TPR_PATH --output_gro_path OUTPUT_GRO_PATH --output_edr_path OUTPUT_EDR_PATH --output_log_path OUTPUT_LOG_PATH [--output_trr_path OUTPUT_TRR_PATH] [--input_cpt_path INPUT_CPT_PATH] [--output_xtc_path OUTPUT_XTC_PATH] [--output_cpt_path OUTPUT_CPT_PATH] [--output_dhdl_path OUTPUT_DHDL_PATH]
Wrapper for the GROMACS mdrun module.
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_tpr_path INPUT_TPR_PATH
Path to the portable binary run input file TPR. Accepted formats: tpr.
--output_gro_path OUTPUT_GRO_PATH
Path to the output GROMACS structure GRO file. Accepted formats: gro.
--output_edr_path OUTPUT_EDR_PATH
Path to the output GROMACS portable energy file EDR. Accepted formats: edr.
--output_log_path OUTPUT_LOG_PATH
Path to the output GROMACS trajectory log file LOG. Accepted formats: log.
optional arguments:
--output_trr_path OUTPUT_TRR_PATH
Path to the GROMACS uncompressed raw trajectory file TRR. Accepted formats: trr.
--input_cpt_path INPUT_CPT_PATH
Path to the input GROMACS checkpoint file CPT. Accepted formats: cpt.
--output_xtc_path OUTPUT_XTC_PATH
Path to the GROMACS compressed trajectory file XTC. Accepted formats: xtc.
--output_cpt_path OUTPUT_CPT_PATH
Path to the output GROMACS checkpoint file CPT. Accepted formats: cpt.
--output_dhdl_path OUTPUT_DHDL_PATH
Path to the output dhdl.xvg file only used when free energy calculation is turned on. Accepted formats: xvg.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_tpr_path (string): Path to the portable binary run input file TPR. File type: input. Sample file. Accepted formats: TPR
output_gro_path (string): Path to the output GROMACS structure GRO file. File type: output. Sample file. Accepted formats: GRO
output_edr_path (string): Path to the output GROMACS portable energy file EDR. File type: output. Sample file. Accepted formats: EDR
output_log_path (string): Path to the output GROMACS trajectory log file LOG. File type: output. Sample file. Accepted formats: LOG
output_trr_path (string): Path to the GROMACS uncompressed raw trajectory file TRR. File type: output. Sample file. Accepted formats: TRR
input_cpt_path (string): Path to the input GROMACS checkpoint file CPT. File type: input. Sample file. Accepted formats: CPT
output_xtc_path (string): Path to the GROMACS compressed trajectory file XTC. File type: output. Sample file. Accepted formats: XTC
output_cpt_path (string): Path to the output GROMACS checkpoint file CPT. File type: output. Sample file. Accepted formats: CPT
output_dhdl_path (string): Path to the output dhdl.xvg file only used when free energy calculation is turned on. File type: output. Sample file. Accepted formats: XVG
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
mpi_bin (string): (None) Path to the MPI runner. Usually “mpirun” or “srun”.
mpi_np (integer): (0) Number of MPI processes. Usually an integer bigger than 1.
mpi_flags (string): (None) Path to the MPI hostlist file.
checkpoint_time (integer): (15) Checkpoint writing interval in minutes. Only enabled if an output_cpt_path is provided.
noappend (boolean): (False) Include the noappend flag to open new output files and add the simulation part number to all output file names
num_threads (integer): (0) Let GROMACS guess. The number of threads that are going to be used.
num_threads_mpi (integer): (0) Let GROMACS guess. The number of GROMACS MPI threads per rank that are going to be used.
num_threads_omp (integer): (0) Let GROMACS guess. The number of GROMACS OPENMP threads per MPI rank that are going to be used.
num_threads_omp_pme (integer): (0) Let GROMACS guess. The number of GROMACS OPENMP_PME threads per MPI rank that are going to be used.
use_gpu (boolean): (False) Use settings appropriate for GPU. Adds: -nb gpu -pme gpu
gpu_id (string): (None) list of unique GPU device IDs available to use.
gpu_tasks (string): (None) list of GPU device IDs, mapping each PP task on each node to a device.
gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable.
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) Path to the binary executable of your container.
container_image (string): (None) Container Image identifier.
container_volume_path (string): (/data) Path to an internal directory in the container.
container_working_dir (string): (None) Path to the internal CWD in the container.
container_user_id (string): (None) User number id to be mapped inside the container.
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell.
YAML
Common config file
properties:
binary_path: gmx
num_threads: 0
Docker config file
properties:
binary_path: gmx
container_image: quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp
num_threads: 0
Singularity config file
properties:
binary_path: gmx
container_image: https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: singularity
container_volume_path: /tmp
container_working_dir: /tmp
num_threads: 0
Command line
mdrun --config config_mdrun.yml --input_tpr_path mdrun.tpr --output_gro_path ref_mdrun.gro --output_edr_path ref_mdrun.edr --output_log_path ref_mdrun.log --output_trr_path ref_mdrun.trr --input_cpt_path input.cpt --output_xtc_path output.xtc --output_cpt_path output.cpt --output_dhdl_path output.xvg
JSON
Common config file
{
"properties": {
"num_threads": 0,
"binary_path": "gmx"
}
}
Docker config file
{
"properties": {
"num_threads": 0,
"binary_path": "gmx",
"container_path": "docker",
"container_image": "quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Singularity config file
{
"properties": {
"num_threads": 0,
"binary_path": "gmx",
"container_path": "singularity",
"container_image": "https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
mdrun --config config_mdrun.json --input_tpr_path mdrun.tpr --output_gro_path ref_mdrun.gro --output_edr_path ref_mdrun.edr --output_log_path ref_mdrun.log --output_trr_path ref_mdrun.trr --input_cpt_path input.cpt --output_xtc_path output.xtc --output_cpt_path output.cpt --output_dhdl_path output.xvg
Mdrun_plumed
Wrapper of the GROMACS mdrun module.
Get help
Command:
mdrun_plumed -h
usage: mdrun_plumed [-h] [-c CONFIG] --input_tpr_path INPUT_TPR_PATH --output_gro_path OUTPUT_GRO_PATH --output_edr_path OUTPUT_EDR_PATH --output_log_path OUTPUT_LOG_PATH [--output_trr_path OUTPUT_TRR_PATH] [--input_cpt_path INPUT_CPT_PATH] [--output_xtc_path OUTPUT_XTC_PATH] [--output_cpt_path OUTPUT_CPT_PATH] [--output_dhdl_path OUTPUT_DHDL_PATH] [--input_plumed_path INPUT_PLUMED_PATH] [--input_plumed_folder INPUT_PLUMED_FOLDER] [--output_plumed_folder OUTPUT_PLUMED_FOLDER]
Wrapper for the GROMACS mdrun with PLUMED module.
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_tpr_path INPUT_TPR_PATH
Path to the portable binary run input file TPR. Accepted formats: tpr.
--output_gro_path OUTPUT_GRO_PATH
Path to the output GROMACS structure GRO file. Accepted formats: gro.
--output_edr_path OUTPUT_EDR_PATH
Path to the output GROMACS portable energy file EDR. Accepted formats: edr.
--output_log_path OUTPUT_LOG_PATH
Path to the output GROMACS trajectory log file LOG. Accepted formats: log.
optional arguments:
--output_trr_path OUTPUT_TRR_PATH
Path to the GROMACS uncompressed raw trajectory file TRR. Accepted formats: trr.
--input_cpt_path INPUT_CPT_PATH
Path to the input GROMACS checkpoint file CPT. Accepted formats: cpt.
--output_xtc_path OUTPUT_XTC_PATH
Path to the GROMACS compressed trajectory file XTC. Accepted formats: xtc.
--output_cpt_path OUTPUT_CPT_PATH
Path to the output GROMACS checkpoint file CPT. Accepted formats: cpt.
--output_dhdl_path OUTPUT_DHDL_PATH
Path to the output dhdl.xvg file only used when free energy calculation is turned on. Accepted formats: xvg.
--input_plumed_path INPUT_PLUMED_PATH
Path to the main PLUMED input file. If provided, PLUMED will be used during the simulation. All files used by the main PLUMED input file must exist in the input_plumed_folder and be called with just their name. Make sure to provide a GROMACS version with the PLUMED patch. Accepted formats: dat.
--input_plumed_folder INPUT_PLUMED_FOLDER
Path to the folder with all files needed by the main PLUMED input file, see input_plumed_path. Accepted formats: directory.
--output_plumed_folder OUTPUT_PLUMED_FOLDER
Folder where PLUMED generated output files will be saved. Accepted formats: directory.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_tpr_path (string): Path to the portable binary run input file TPR. File type: input. Sample file. Accepted formats: TPR
output_gro_path (string): Path to the output GROMACS structure GRO file. File type: output. Sample file. Accepted formats: GRO
output_edr_path (string): Path to the output GROMACS portable energy file EDR. File type: output. Sample file. Accepted formats: EDR
output_log_path (string): Path to the output GROMACS trajectory log file LOG. File type: output. Sample file. Accepted formats: LOG
output_trr_path (string): Path to the GROMACS uncompressed raw trajectory file TRR. File type: output. Sample file. Accepted formats: TRR
input_cpt_path (string): Path to the input GROMACS checkpoint file CPT. File type: input. Sample file. Accepted formats: CPT
output_xtc_path (string): Path to the GROMACS compressed trajectory file XTC. File type: output. Sample file. Accepted formats: XTC
output_cpt_path (string): Path to the output GROMACS checkpoint file CPT. File type: output. Sample file. Accepted formats: CPT
output_dhdl_path (string): Path to the output dhdl.xvg file only used when free energy calculation is turned on. File type: output. Sample file. Accepted formats: XVG
input_plumed_path (string): Path to the main PLUMED input file. If provided, PLUMED will be used during the simulation. All files used by the main PLUMED input file must exist in the input_plumed_folder and be called with just their name. Make sure to provide a GROMACS version with the PLUMED patch. File type: input. Sample file. Accepted formats: DAT
input_plumed_folder (dir): Path to the folder with all files needed by the main PLUMED input file, see input_plumed_path. File type: input. Sample file. Accepted formats: DIRECTORY
output_plumed_folder (dir): Folder where PLUMED generated output files will be saved. File type: output. Sample file. Accepted formats: DIRECTORY
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
mpi_bin (string): (None) Path to the MPI runner. Usually “mpirun” or “srun”.
mpi_np (integer): (0) Number of MPI processes. Usually an integer bigger than 1.
mpi_flags (string): (None) Path to the MPI hostlist file.
checkpoint_time (integer): (15) Checkpoint writing interval in minutes. Only enabled if an output_cpt_path is provided.
noappend (boolean): (False) Include the noappend flag to open new output files and add the simulation part number to all output file names
num_threads (integer): (0) Let GROMACS guess. The number of threads that are going to be used.
num_threads_mpi (integer): (0) Let GROMACS guess. The number of GROMACS MPI threads that are going to be used.
num_threads_omp (integer): (0) Let GROMACS guess. The number of GROMACS OPENMP threads that are going to be used.
num_threads_omp_pme (integer): (0) Let GROMACS guess. The number of GROMACS OPENMP_PME threads that are going to be used.
use_gpu (boolean): (False) Use settings appropriate for GPU. Adds: -nb gpu -pme gpu
gpu_id (string): (None) list of unique GPU device IDs available to use.
gpu_tasks (string): (None) list of GPU device IDs, mapping each PP task on each node to a device.
gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable.
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) Path to the binary executable of your container.
container_image (string): (None) Container Image identifier.
container_volume_path (string): (/data) Path to an internal directory in the container.
container_working_dir (string): (None) Path to the internal CWD in the container.
container_user_id (string): (None) User number id to be mapped inside the container.
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell.
YAML
Common config file
properties:
binary_path: gmx
num_threads: 0
Command line
mdrun_plumed --config config_mdrun_plumed.yml --input_tpr_path mdrun.tpr --output_gro_path ref_mdrun.gro --output_edr_path ref_mdrun.edr --output_log_path ref_mdrun.log --output_trr_path ref_mdrun.trr --input_cpt_path input.cpt --output_xtc_path output.xtc --output_cpt_path output.cpt --output_dhdl_path output.xvg --input_plumed_path input.dat --input_plumed_folder input.directory --output_plumed_folder output.directory
JSON
Common config file
{
"properties": {
"num_threads": 0,
"binary_path": "gmx"
}
}
Command line
mdrun_plumed --config config_mdrun_plumed.json --input_tpr_path mdrun.tpr --output_gro_path ref_mdrun.gro --output_edr_path ref_mdrun.edr --output_log_path ref_mdrun.log --output_trr_path ref_mdrun.trr --input_cpt_path input.cpt --output_xtc_path output.xtc --output_cpt_path output.cpt --output_dhdl_path output.xvg --input_plumed_path input.dat --input_plumed_folder input.directory --output_plumed_folder output.directory
Ndx2resttop
Generate a restrained topology from an index NDX file.
Get help
Command:
ndx2resttop -h
usage: ndx2resttop [-h] [-c CONFIG] --input_ndx_path INPUT_NDX_PATH --input_top_zip_path INPUT_TOP_ZIP_PATH -o OUTPUT_TOP_ZIP_PATH
Generate a restrained topology from an index NDX 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_ndx_path INPUT_NDX_PATH
Path to the input NDX index file. Accepted formats: ndx.
--input_top_zip_path INPUT_TOP_ZIP_PATH
Path the input TOP topology in zip format. Accepted formats: zip.
-o OUTPUT_TOP_ZIP_PATH, --output_top_zip_path OUTPUT_TOP_ZIP_PATH
Path the output TOP topology in zip format. Accepted formats: zip.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_ndx_path (string): Path to the input NDX index file. File type: input. Sample file. Accepted formats: NDX
input_top_zip_path (string): Path the input TOP topology in zip format. File type: input. Sample file. Accepted formats: ZIP
output_top_zip_path (string): Path the output TOP topology in zip format. File type: output. Sample file. Accepted formats: ZIP
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
posres_names (string): (CUSTOM_POSRES) Space-separated preprocessor macro names, one per triplet (e.g.
"CHAIN_A_POSRES CHAIN_B_POSRES"). Activated at grompp time via-D <name>. Must match the length of ref_rest_mol_triplet_list.force_constants (string): (500 500 500) Three space-separated force constants Fx Fy Fz in kJ/mol/nm². Written verbatim into each ITP line so the same value is applied to every restrained atom.
ref_rest_mol_triplet_list (string): (None) Comma-separated triplets
(reference_group, restrain_group, molecule_name), one per molecule to restrain.reference_group: NDX group containing all atoms of the molecule in global (system-wide) GROMACS numbering. Used only as a coordinate frame to convert global indices to molecule-local 1-based indices. Example:r_1-9280.restrain_group: NDX group with the subset of atoms to actually restrain (must be a strict subset of reference_group). Example:P_&_r_1-9280.molecule_name: the[ moleculetype ]name in the topology used to locate where to splice the#ifdefblock. Example:1TSR.
YAML
Common config file
properties:
ref_rest_mol_triplet_list: ( Chain_A, Chain_A_noMut, A ), ( Chain_B, Chain_B_noMut,
B ), ( Chain_C, Chain_C_noMut, C ), ( Chain_D, Chain_D_noMut, D )
Command line
ndx2resttop --config config_ndx2resttop.yml --input_ndx_path ndx2resttop.ndx --input_top_zip_path ndx2resttop.zip --output_top_zip_path ref_ndx2resttop.zip
JSON
Common config file
{
"properties": {
"ref_rest_mol_triplet_list": "( Chain_A, Chain_A_noMut, A ), ( Chain_B, Chain_B_noMut, B ), ( Chain_C, Chain_C_noMut, C ), ( Chain_D, Chain_D_noMut, D )"
}
}
Command line
ndx2resttop --config config_ndx2resttop.json --input_ndx_path ndx2resttop.ndx --input_top_zip_path ndx2resttop.zip --output_top_zip_path ref_ndx2resttop.zip
Pdb2gmx
Wrapper class for the GROMACS pdb2gmx module.
Get help
Command:
pdb2gmx -h
usage: pdb2gmx [-h] [-c CONFIG] -i INPUT_PDB_PATH --output_gro_path OUTPUT_GRO_PATH --output_top_zip_path OUTPUT_TOP_ZIP_PATH
Wrapper for the GROMACS pdb2gmx module.
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_PDB_PATH, --input_pdb_path INPUT_PDB_PATH
Path to the input PDB file. Accepted formats: pdb.
--output_gro_path OUTPUT_GRO_PATH
Path to the output GRO file. Accepted formats: gro.
--output_top_zip_path OUTPUT_TOP_ZIP_PATH
Path the output TOP topology in zip format. Accepted formats: zip.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_pdb_path (string): Path to the input PDB file. File type: input. Sample file. Accepted formats: PDB
output_gro_path (string): Path to the output GRO file. File type: output. Sample file. Accepted formats: GRO
output_top_zip_path (string): Path the output TOP topology in zip format. File type: output. Sample file. Accepted formats: ZIP
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
water_type (string): (spce) Water molecule type.
force_field (string): (amber99sb-ildn) Force field to be used during the conversion.
ignh (boolean): (False) Should pdb2gmx ignore the hydrogens in the original structure.
lys (array): (None) Lysine protonation states for each chain in the input pdb. Each item of the list should be a string with the protonation states for that chain or empty if the residue is not present in that chain (0: not protonated, 1: protonated).
arg (array): (None) Arginine protonation states for each chain in the input pdb. Each item of the list should be a string with the protonation states for that chain or empty if the residue is not present in that chain (0: not protonated, 1: protonated).
asp (array): (None) Aspartic acid protonation states for each chain in the input pdb. Each item of the list should be a string with the protonation states for that chain or empty if the residue is not present in that chain (0: not protonated, 1: protonated).
glu (array): (None) Glutamic acid protonation states for each chain in the input pdb. Each item of the list should be a string with the protonation states for that chain or empty if the residue is not present in that chain (0: not protonated, 1: protonated).
gln (array): (None) Glutamine protonation states for each chain in the input pdb. Each item of the list should be a string with the protonation states for that chain or empty if the residue is not present in that chain (0: not protonated, 1: protonated).
his (array): (None) Histidine protonation states for each chain in the input pdb. Each item of the list should be a string with the protonation states for that chain or empty if the residue is not present in that chain. Make sure residues are named HIS (0: HID, 1: HIE, 2: HIP, 3: HIS1).
merge (boolean): (False) Merge all chains into a single molecule.
gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable.
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) Path to the binary executable of your container.
container_image (string): (gromacs/gromacs:latest) Container Image identifier.
container_volume_path (string): (/data) Path to an internal directory in the container.
container_working_dir (string): (None) Path to the internal CWD in the container.
container_user_id (string): (None) User number id to be mapped inside the container.
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell.
YAML
Common config file
properties:
his: 0 0 1 1 0 0 0
Docker config file
properties:
container_image: quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp
his: 0 0 1 1 0 0 0
Singularity config file
properties:
container_image: https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: singularity
container_volume_path: /tmp
container_working_dir: /tmp
his: 0 0 1 1 0 0 0
Command line
pdb2gmx --config config_pdb2gmx.yml --input_pdb_path egfr.pdb --output_gro_path ref_pdb2gmx.gro --output_top_zip_path ref_pdb2gmx.zip
JSON
Common config file
{
"properties": {
"his": "0 0 1 1 0 0 0"
}
}
Docker config file
{
"properties": {
"his": "0 0 1 1 0 0 0",
"container_path": "docker",
"container_image": "quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Singularity config file
{
"properties": {
"his": "0 0 1 1 0 0 0",
"container_path": "singularity",
"container_image": "https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
pdb2gmx --config config_pdb2gmx.json --input_pdb_path egfr.pdb --output_gro_path ref_pdb2gmx.gro --output_top_zip_path ref_pdb2gmx.zip
Solvate
Wrapper of the GROMACS solvate module.
Get help
Command:
solvate -h
usage: solvate [-h] [-c CONFIG] --input_solute_gro_path INPUT_SOLUTE_GRO_PATH --output_gro_path OUTPUT_GRO_PATH --input_top_zip_path INPUT_TOP_ZIP_PATH --output_top_zip_path OUTPUT_TOP_ZIP_PATH [--input_solvent_gro_path INPUT_SOLVENT_GRO_PATH]
Wrapper for the GROMACS solvate module.
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_solute_gro_path INPUT_SOLUTE_GRO_PATH
Path to the input GRO file. Accepted formats: gro, pdb.
--output_gro_path OUTPUT_GRO_PATH
Path to the output GRO file. Accepted formats: gro, pdb.
--input_top_zip_path INPUT_TOP_ZIP_PATH
Path the input TOP topology in zip format. Accepted formats: zip.
--output_top_zip_path OUTPUT_TOP_ZIP_PATH
Path the output topology in zip format. Accepted formats: zip.
optional arguments:
--input_solvent_gro_path INPUT_SOLVENT_GRO_PATH
(spc216.gro) Path to the GRO file containing the structure of the solvent. Accepted formats: gro.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_solute_gro_path (string): Path to the input GRO file. File type: input. Sample file. Accepted formats: GRO, PDB
output_gro_path (string): Path to the output GRO file. File type: output. Sample file. Accepted formats: GRO, PDB
input_top_zip_path (string): Path the input TOP topology in zip format. File type: input. Sample file. Accepted formats: ZIP
output_top_zip_path (string): Path the output topology in zip format. File type: output. Sample file. Accepted formats: ZIP
input_solvent_gro_path (string): (spc216.gro) Path to the GRO file containing the structure of the solvent. File type: input. Sample file. Accepted formats: GRO
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
shell (number): (0.0) Thickness in nanometers of optional water layer around solute.
gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable.
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) Path to the binary executable of your container.
container_image (string): (gromacs/gromacs:latest) Container Image identifier.
container_volume_path (string): (/data) Path to an internal directory in the container.
container_working_dir (string): (None) Path to the internal CWD in the container.
container_user_id (string): (None) User number id to be mapped inside the container.
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell.
YAML
Common config file
properties:
binary_path: gmx
restart: 'False'
Docker config file
properties:
binary_path: gmx
container_image: quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp
restart: 'False'
Singularity config file
properties:
binary_path: gmx
container_image: https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: singularity
container_volume_path: /tmp
container_working_dir: /tmp
restart: 'False'
Command line
solvate --config config_solvate.yml --input_solute_gro_path solvate.gro --output_gro_path ref_solvate.gro --input_top_zip_path solvate.zip --output_top_zip_path ref_solvate.zip --input_solvent_gro_path input.gro
JSON
Common config file
{
"properties": {
"binary_path": "gmx",
"restart": "False"
}
}
Docker config file
{
"properties": {
"binary_path": "gmx",
"restart": "False",
"container_path": "docker",
"container_image": "quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Singularity config file
{
"properties": {
"binary_path": "gmx",
"restart": "False",
"container_path": "singularity",
"container_image": "https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
solvate --config config_solvate.json --input_solute_gro_path solvate.gro --output_gro_path ref_solvate.gro --input_top_zip_path solvate.zip --output_top_zip_path ref_solvate.zip --input_solvent_gro_path input.gro
Trjcat
Wrapper class for the GROMACS trjcat module.
Get help
Command:
trjcat -h
usage: trjcat [-h] [-c CONFIG] -i INPUT_TRJ_ZIP_PATH -o OUTPUT_TRJ_PATH
Wrapper for the GROMACS trjcat module.
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_TRJ_ZIP_PATH, --input_trj_zip_path INPUT_TRJ_ZIP_PATH
Path the input GROMACS trajectories (xtc, trr, cpt, gro, pdb, tng) to concatenate in zip format. Accepted formats: zip.
-o OUTPUT_TRJ_PATH, --output_trj_path OUTPUT_TRJ_PATH
Path to the output trajectory file. Accepted formats: pdb, gro, xtc, trr, tng.
I / O Arguments
Syntax: input_argument (datatype) : Definition
Config input / output arguments for this building block:
input_trj_zip_path (string): Path the input GROMACS trajectories (xtc, trr, cpt, gro, pdb, tng) to concatenate in zip format. File type: input. Sample file. Accepted formats: ZIP
output_trj_path (string): Path to the output trajectory file. File type: output. Sample file. Accepted formats: PDB, GRO, XTC, TRR, TNG
Config
Syntax: input_parameter (datatype) - (default_value) Definition
Config parameters for this building block:
concatenate (boolean): (True) Only concatenate the files without removal of frames with identical timestamps.
gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable.
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) Path to the binary executable of your container.
container_image (string): (None) Container Image identifier.
container_volume_path (string): (/data) Path to an internal directory in the container.
container_working_dir (string): (None) Path to the internal CWD in the container.
container_user_id (string): (None) User number id to be mapped inside the container.
container_shell_path (string): (/bin/bash) Path to the binary executable of the container shell.
YAML
Common config file
properties:
binary_path: gmx
restart: 'False'
Docker config file
properties:
binary_path: gmx
container_image: quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: docker
container_volume_path: /tmp
container_working_dir: /tmp
restart: 'False'
Singularity config file
properties:
binary_path: gmx
container_image: https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0
container_path: singularity
container_volume_path: /tmp
container_working_dir: /tmp
restart: 'False'
Command line
trjcat --config config_trjcat.yml --input_trj_zip_path trjcat.zip --output_trj_path ref_trjcat.trr
JSON
Common config file
{
"properties": {
"binary_path": "gmx",
"restart": "False"
}
}
Docker config file
{
"properties": {
"binary_path": "gmx",
"restart": "False",
"container_path": "docker",
"container_image": "quay.io/biocontainers/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Singularity config file
{
"properties": {
"binary_path": "gmx",
"restart": "False",
"container_path": "singularity",
"container_image": "https://depot.galaxyproject.org/singularity/biobb_gromacs:5.2.1--pyhdfd78af_0",
"container_volume_path": "/tmp",
"container_working_dir": "/tmp"
}
}
Command line
trjcat --config config_trjcat.json --input_trj_zip_path trjcat.zip --output_trj_path ref_trjcat.trr