adaptivemastermsm.launcher.launcher module

This file is part of the AdaptiveMasterMSM package.

class adaptivemastermsm.launcher.launcher.Launcher(simsys)[source]

Bases: object

Call GROMACS and process output to pass it to class analyzer

gen_tpr(mdp=None, tpr='data/out.tpr', nsteps=250000)[source]

Function for generating tpr files

Parameters:
  • mdp (str) – The parameter input file
  • tpr (str) – The Gromacs run input file
gmx_run(out='data/out')[source]

Runs MD simulations using gmx mdrun

Parameters:
  • tpr (str) – Gromacs run input file
  • out (str) – Root filename for output
gmx_worker(x)[source]

mp worker for running Gromacs jobs

–>Shall we use ‘multi’ flag from Gromacs?

Parameters:x (list) – List containing input for each mp worker. Includes: path to tpr file path to inp/out file
mp_run(tprs, outs)[source]

Driver for gmx_worker

adaptivemastermsm.launcher.launcher_lib module

This file is part of the AdaptiveMasterMSM package.

adaptivemastermsm.launcher.launcher_lib.checkfile(inp)[source]
adaptivemastermsm.launcher.launcher_lib.write_mdp_min(emstep=0.001, nsteps=50000, constraints='none')[source]
adaptivemastermsm.launcher.launcher_lib.write_mdp_npt(dt=0.002, nsteps=50000, constraints='h-bonds', ref_t=300, ref_p=1.0)[source]
adaptivemastermsm.launcher.launcher_lib.write_mdp_nvt(dt=0.002, nsteps=50000, constraints='h-bonds', ref_t=300)[source]
adaptivemastermsm.launcher.launcher_lib.write_mdp_prod(emstep=0.002, nsteps=50000, constraints='h-bonds')[source]

Module contents