pmemd package

Submodules

pmemd.pmemd_mdrun module

Module containing the PmemdMDRun class and the command line interface.

class pmemd.pmemd_mdrun.PmemdMDRun(input_top_path: str, input_crd_path: str, output_log_path: str, output_traj_path: str, output_rst_path: str, input_ref_path: Optional[str] = None, input_mdin_path: Optional[str] = None, input_cpin_path: Optional[str] = None, output_cpout_path: Optional[str] = None, output_cprst_path: Optional[str] = None, output_mdinfo_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs)[source]

Bases: biobb_common.generic.biobb_object.BiobbObject

biobb_amber PmemdMDRun
Runs molecular dynamics using pmemd tool from the AMBER MD package.
Parameters
  • input_top_path (str) – Input topology file (AMBER ParmTop). File type: input. Sample file. Accepted formats: top (edam:format_3881), parmtop (edam:format_3881), prmtop (edam:format_3881).

  • input_crd_path (str) –

    Input coordinates file (AMBER crd). File type: input. Sample file. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878), rst (edam:format_3886), rst7 (edam:format_3886), netcdf (edam:format_3650), nc (edam:format_3650), ncrst (edam:format_3886).

  • input_mdin_path (str) (Optional) –

    Input configuration file (MD run options) (AMBER mdin). File type: input. Sample file. Accepted formats: mdin (edam:format_2330), in (edam:format_2330), txt (edam:format_2330).

  • input_cpin_path (str) (Optional) –

    Input constant pH file (AMBER cpin). File type: input. Sample file. Accepted formats: cpin (edam:format_2330).

  • input_ref_path (str) (Optional) –

    Input reference coordinates for position restraints. File type: input. Sample file. Accepted formats: crd (edam:format_3878), mdcrd (edam:format_3878), inpcrd (edam:format_3878), rst (edam:format_3886), rst7 (edam:format_3886), netcdf (edam:format_3650), nc (edam:format_3650), ncrst (edam:format_3886).

  • output_log_path (str) –

    Output log file. File type: output. Sample file. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).

  • output_traj_path (str) –

    Output trajectory file. File type: output. Sample file. Accepted formats: trj (edam:format_3878), crd (edam:format_3878), mdcrd (edam:format_3878), x (edam:format_3878), netcdf (edam:format_3650), nc (edam:format_3650).

  • output_rst_path (str) –

    Output restart file. File type: output. Sample file. Accepted formats: rst (edam:format_3886), rst7 (edam:format_3886), netcdf (edam:format_3650), nc (edam:format_3650), ncrst (edam:format_3886).

  • output_cpout_path (str) (Optional) –

    Output constant pH file (AMBER cpout). File type: output. Sample file. Accepted formats: cpout (edam:format_2330).

  • output_cprst_path (str) (Optional) –

    Output constant pH restart file (AMBER rstout). File type: output. Sample file. Accepted formats: cprst (edam:format_3886), rst (edam:format_3886), rst7 (edam:format_3886).

  • output_mdinfo_path (str) (Optional) –

    Output MD info. File type: output. Sample file. Accepted formats: mdinfo (edam:format_2330).

  • properties (dict - Python dictionary object containing the tool parameters, not input/output files) –

    • mdin (dict) - ({}) pmemd MD run options specification. (Used if input_mdin_path is None)

    • pmemd_path (str) - (“pmemd”) pmemd binary path to be used.

    • simulation_type (str) - (“minimization”) Default options for the mdin file. Each creates a different mdin file. Values: minimization (Runs an energy minimization), min_vacuo (Runs an energy minimization in vacuo), NVT (Runs an NVT equilibration), npt (Runs an NPT equilibration), free (Runs a MD simulation).

    • mpi_bin (str) - (None) Path to the MPI runner. Usually “mpirun” or “srun”.

    • mpi_np (int) - (0) [0~1000|1] Number of MPI processes. Usually an integer bigger than 1.

    • mpi_flags (str) - (None) Path to the MPI hostlist file.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

Examples

This is a use example of how to use the building block from Python:

from biobb_amber.pmemd.pmemd_mdrun import pmemd_mdrun
prop = {
    'simulation_type' : 'npt',
    'mdin' : {
        'dt' : 0.002
    }
}
pmemd_mdrun(input_top_path='/path/to/topology.top',
             input_crd_path='/path/to/coordinates.crd',
             output_traj_path='/path/to/newTrajectory.crd',
             output_rst_path='/path/to/newRestart.rst',
             output_log_path='/path/to/newAmberlog.log',
             properties=prop)
Info:
check_data_params(out_log, err_log)[source]

Checks input/output paths correctness

create_mdin(path: Optional[str] = None) str[source]

Creates an AMBER MD configuration file (mdin) using the properties file settings

launch()[source]

Launches the execution of the PmemdMDRun module.

pmemd.pmemd_mdrun.main()[source]
pmemd.pmemd_mdrun.pmemd_mdrun(input_top_path: str, input_crd_path: str, output_log_path: str, output_traj_path: str, output_rst_path: str, input_mdin_path: Optional[str] = None, input_cpin_path: Optional[str] = None, output_cpout_path: Optional[str] = None, output_cprst_path: Optional[str] = None, output_mdinfo_path: Optional[str] = None, input_ref_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) int[source]

Create PmemdMDRun method