BioBB MD Command Line Help

Generic usage:

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

Mdrun

Wrapper of the GROMACS mdrun module.

Get help

Command:

mdrun -h
/bin/sh: mdrun: command not found

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_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
  • 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..
  • 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..
  • gmx_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..
  • 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:
  gmx_path: gmx
  num_threads: 0

Docker config file

properties:
  container_image: longr/gromacs-docker:latest
  container_path: docker
  container_volume_path: /inout

Singularity config file

properties:
  container_image: gromacs.simg
  container_path: singularity
  container_volume_path: /inout

Command line

mdrun --config config_mdrun.yml --input_tpr_path mdrun.tpr --output_trr_path ref_mdrun.trr --output_gro_path ref_mdrun.gro --output_edr_path ref_mdrun.edr --output_log_path ref_mdrun.log --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,
    "gmx_path": "gmx"
  }
}

Docker config file

{
  "properties": {
    "container_path": "docker",
    "container_image": "longr/gromacs-docker:latest",
    "container_volume_path": "/inout"
  }
}

Singularity config file

{
  "properties": {
    "container_path": "singularity",
    "container_image": "gromacs.simg",
    "container_volume_path": "/inout"
  }
}

Command line

mdrun --config config_mdrun.json --input_tpr_path mdrun.tpr --output_trr_path ref_mdrun.trr --output_gro_path ref_mdrun.gro --output_edr_path ref_mdrun.edr --output_log_path ref_mdrun.log --input_cpt_path input.cpt --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
/bin/sh: make_ndx: command 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 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..
  • gmx_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..
  • 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 CA C N O

Docker config file

properties:
  container_image: longr/gromacs-docker:latest
  container_path: docker
  container_volume_path: /tmp

Singularity config file

properties:
  container_image: gromacs.simg
  container_path: singularity
  container_volume_path: /tmp

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 CA C N O"
  }
}

Docker config file

{
  "properties": {
    "container_path": "docker",
    "container_image": "longr/gromacs-docker:latest",
    "container_volume_path": "/tmp"
  }
}

Singularity config file

{
  "properties": {
    "container_path": "singularity",
    "container_image": "gromacs.simg",
    "container_volume_path": "/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

Editconf

Wrapper class for the GROMACS editconf module.

Get help

Command:

editconf -h
/bin/sh: editconf: command not found

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
  • output_gro_path (string): Path to the output GRO file. File type: output. Sample file. Accepted formats: 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_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..
  • gmx_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..
  • 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:
  box_type: cubic
  distance_to_molecule: 1.0

Docker config file

properties:
  container_image: longr/gromacs-docker:latest
  container_path: docker
  container_volume_path: /tmp

Singularity config file

properties:
  container_image: gromacs.simg
  container_path: singularity
  container_volume_path: /tmp

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": {
    "container_path": "docker",
    "container_image": "longr/gromacs-docker:latest",
    "container_volume_path": "/tmp"
  }
}

Singularity config file

{
  "properties": {
    "container_path": "singularity",
    "container_image": "gromacs.simg",
    "container_volume_path": "/tmp"
  }
}

Command line

editconf --config config_editconf.json --input_gro_path editconf.gro --output_gro_path ref_editconf.gro

Ndx2resttop

Generate a restrained topology from an index NDX file.

Get help

Command:

ndx2resttop -h
/bin/sh: ndx2resttop: command not found

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:

  • force_constants (string): (500 500 500) Array of three floats defining the force constants..
  • ref_rest_chain_triplet_list (string): (None) Triplet list composed by (reference group, restrain group, chain) list..

YAML

Common config file

properties:
  ref_rest_chain_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_chain_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

Grompp

Wrapper of the GROMACS grompp module.

Get help

Command:

grompp -h
/bin/sh: grompp: command not found

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..
  • gmx_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..
  • 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: gromacs/gromacs:latest
  container_path: docker
  container_volume_path: /inout
  container_working_dir: /inout
  maxwarn: 1
  mdp:
    ld-seed: '1'

Singularity config file

properties:
  container_image: gromacs.simg
  container_path: singularity
  container_volume_path: /inout
  container_working_dir: /inout
  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": "gromacs/gromacs:latest",
    "container_volume_path": "/inout",
    "container_working_dir": "/inout"
  }
}

Singularity config file

{
  "properties": {
    "maxwarn": 1,
    "mdp": {
      "ld-seed": "1"
    },
    "container_path": "singularity",
    "container_image": "gromacs.simg",
    "container_volume_path": "/inout",
    "container_working_dir": "/inout"
  }
}

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

Gmxselect

Wrapper of the GROMACS select module.

Get help

Command:

gmxselect -h
/bin/sh: gmxselect: command 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 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..
  • gmx_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..
  • 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: gromacs/gromacs:latest
  container_path: docker
  container_volume_path: /inout
  selection: \"Mynewgroup\" group \"Protein-H\" and not same residue as within 0.4
    of resname ARG

Singularity config file

properties:
  container_image: gromacs.simg
  container_path: singularity
  container_volume_path: /inout
  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": "gromacs/gromacs:latest",
    "container_volume_path": "/inout"
  }
}

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": "gromacs.simg",
    "container_volume_path": "/inout"
  }
}

Command line

gmxselect --config config_gmxselect.json --input_structure_path make_ndx.tpr --output_ndx_path ref_select.ndx --input_ndx_path input.ndx

Pdb2gmx

Wrapper class for the GROMACS pdb2gmx module.

Get help

Command:

pdb2gmx -h
/bin/sh: pdb2gmx: command not found

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 hidrogens in the original structure..
  • his (string): (None) Histidine protonation array..
  • merge (boolean): (False) Merge all chains into a single molecule..
  • gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable..
  • gmx_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..
  • 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: longr/gromacs-docker:latest
  container_path: docker
  container_volume_path: /inout
  his: 0 0 1 1 0 0 0

Singularity config file

properties:
  container_image: gromacs.simg
  container_path: singularity
  container_volume_path: /inout
  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": "longr/gromacs-docker:latest",
    "container_volume_path": "/inout"
  }
}

Singularity config file

{
  "properties": {
    "his": "0 0 1 1 0 0 0",
    "container_path": "singularity",
    "container_image": "gromacs.simg",
    "container_volume_path": "/inout"
  }
}

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

Append_ligand

This class takes a ligand ITP file and inserts it in a topology.

Get help

Command:

append_ligand -h
/bin/sh: append_ligand: command not found

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..

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

Solvate

Wrapper of the GROMACS solvate module.

Get help

Command:

solvate -h
/bin/sh: solvate: command not found

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
  • output_gro_path (string): Path to the output 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 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..
  • gmx_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..
  • 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:
  gmx_path: gmx
  restart: 'False'

Docker config file

properties:
  container_image: longr/gromacs-docker:latest
  container_path: docker
  container_volume_path: /inout

Singularity config file

properties:
  container_image: gromacs.simg
  container_path: singularity
  container_volume_path: /inout

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": {
    "gmx_path": "gmx",
    "restart": "False"
  }
}

Docker config file

{
  "properties": {
    "container_path": "docker",
    "container_image": "longr/gromacs-docker:latest",
    "container_volume_path": "/inout"
  }
}

Singularity config file

{
  "properties": {
    "container_path": "singularity",
    "container_image": "gromacs.simg",
    "container_volume_path": "/inout"
  }
}

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

Genion

Wrapper class for the GROMACS genion module.

Get help

Command:

genion -h
/bin/sh: genion: command not found

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..
  • concentration (number): (0.05) Concentration of the ions in (mol/liter)..
  • seed (integer): (1993) Seed for random number generator..
  • gmx_lib (string): (None) Path set GROMACS GMXLIB environment variable..
  • gmx_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..
  • 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:
  container_image: longr/gromacs-docker:latest
  container_path: docker
  container_volume_path: /data
  container_working_dir: /data

Singularity config file

properties:
  container_image: gromacs.simg
  container_path: singularity
  container_volume_path: /data
  container_working_dir: /data

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": {
    "container_path": "docker",
    "container_image": "longr/gromacs-docker:latest",
    "container_volume_path": "/data",
    "container_working_dir": "/data"
  }
}

Singularity config file

{
  "properties": {
    "container_path": "singularity",
    "container_image": "gromacs.simg",
    "container_volume_path": "/data",
    "container_working_dir": "/data"
  }
}

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

Grompp_mdrun

Wrapper of the GROMACS grompp module and the GROMACS mdrun module.

Get help

Command:

grompp_mdrun -h
/bin/sh: grompp_mdrun: command not found

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..
  • gmx_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..
  • 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:
  gmx_path: gmx
  maxwarn: 1
  mdp:
    dt: 0.0001
    ld-seed: '1'
  num_threads: 0
  simulation_type: free

Docker config file

properties:
  container_image: longr/gromacs-docker:latest
  container_path: docker
  container_volume_path: /inout
  gmx_path: gmx
  maxwarn: 1
  mdp:
    dt: 0.0001
    ld-seed: '1'
  num_threads: 0
  simulation_type: free

Singularity config file

properties:
  container_image: gromacs.simg
  container_path: singularity
  container_volume_path: /inout
  gmx_path: gmx
  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,
    "gmx_path": "gmx"
  }
}

Docker config file

{
  "properties": {
    "simulation_type": "free",
    "maxwarn": 1,
    "mdp": {
      "ld-seed": "1",
      "dt": 0.0001
    },
    "num_threads": 0,
    "gmx_path": "gmx",
    "container_path": "docker",
    "container_image": "longr/gromacs-docker:latest",
    "container_volume_path": "/inout"
  }
}

Singularity config file

{
  "properties": {
    "simulation_type": "free",
    "mdp": {
      "ld-seed": "1",
      "dt": 0.0001
    },
    "num_threads": 0,
    "gmx_path": "gmx",
    "container_path": "singularity",
    "container_image": "gromacs.simg",
    "container_volume_path": "/inout"
  }
}

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

Genrestr

Wrapper of the GROMACS genrestr module.

Get help

Command:

genrestr -h
/bin/sh: genrestr: command 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 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..
  • gmx_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..
  • 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: longr/gromacs-docker:latest
  container_path: docker
  container_volume_path: /data
  container_working_dir: /data

Singularity config file

properties:
  container_image: gromacs.simg
  container_path: singularity
  container_volume_path: /data
  container_working_dir: /data

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": {
    "container_path": "docker",
    "container_image": "longr/gromacs-docker:latest",
    "container_volume_path": "/data",
    "container_working_dir": "/data"
  }
}

Singularity config file

{
  "properties": {
    "container_path": "singularity",
    "container_image": "gromacs.simg",
    "container_volume_path": "/data",
    "container_working_dir": "/data"
  }
}

Command line

genrestr --config config_genrestr.json --input_structure_path genrestr.gro --output_itp_path ref_genrestr.itp --input_ndx_path genrestr.ndx