launcher package

adaptivemastermsm.launcher.launcher module

This file is part of the AdaptiveMasterMSM package.

class adaptivemastermsm.launcher.launcher.Launcher(simsys)

Bases: object

Call GROMACS and process output to pass it to class analyzer

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

Function for generating tpr files

Parameters:

• mdp (str) – The parameter input file
• tpr (str) – The Gromacs run input file

gmx_run(out='data/out')

Runs MD simulations using gmx mdrun

Parameters:

• tpr (str) – Gromacs run input file
• out (str) – Root filename for output

gmx_worker(x)

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)

Driver for gmx_worker

adaptivemastermsm.launcher.launcher_lib module

This file is part of the AdaptiveMasterMSM package.

adaptivemastermsm.launcher.launcher_lib.checkfile(inp)

adaptivemastermsm.launcher.launcher_lib.write_mdp_min(emstep=0.001, nsteps=50000, constraints='none')

adaptivemastermsm.launcher.launcher_lib.write_mdp_npt(dt=0.002, nsteps=50000, constraints='h-bonds', ref_t=300, ref_p=1.0)

adaptivemastermsm.launcher.launcher_lib.write_mdp_nvt(dt=0.002, nsteps=50000, constraints='h-bonds', ref_t=300)

adaptivemastermsm.launcher.launcher_lib.write_mdp_prod(emstep=0.002, nsteps=50000, constraints='h-bonds')

Module contents