autosolvate.generatetrajs.startmd

autosolvate.generatetrajs.startmd(argumentList)

Wrap function that parses command line options for autosolvate clustergen, generates inputfiles for Amber and TeraChem, runs MM and QMMM stages. Currently some simulation parameters like simulation time step, integrator type, nonbonded cutoff, thermostat type, Langevin collision frequency, barostat type, pressure relaxation time and frequency of trajectory writing can not be changed from default values by the user.

Parameters

argumentList (list) – The list contains the command line options to specify MM and QMMM stage options.

Command line options:

-f, --filename

prefix of .prmtop and .inpcrd files

-t, --temp

temperature in Kelvin to equilibrate

-p, --pressure

pressure in bar to equilibrate during MM NPT step

-i, --stepsmmmin

Number of MM minimization steps

-m, --stepsmmheat

Number of MM heating steps, setting to 0 skips the MM heating step

-b, --stepsmmnve

Number of MM NVE steps, setting to 0 skips the MM NVE step

-n, --stepsmmnpt

Number of MM NPT steps, setting to 0 skips the MM NPT step

-l, --stepsqmmmmin

Number of QMMM minimization steps, setting to 0 skips the QMMM minimization step

-o, --stepsqmmmheat

Number of QMMM heating steps, setting to 0 skips the QMMM heating step

-v, --stepsqmmmnve

Number of QMMM NVE steps, setting to 0 skips the QMMM NVE step

-s, --stepsqmmmnvt

Number of QMMM NVT steps, setting to 0 skips the QMMM NVT step

-q, --charge

Total charge of system

-u, --spinmultiplicity

Spin multiplicity of whole system

-k, --functional

DFT functional to use for the QM part in QM/MM

-r, --srunuse

option to run inside a slurm job

-x, --pmemduse

Speed up MM with pmemd.CUDA instead of sander

-d, --dryrun

Dry run mode: only generate the commands to run MD programs and save them into a file without executing the command

-h, --help

short usage description

Returns

Generate MD simulation input files and execute MD programs, or same the MD program execution commands in runMM.sh and runQMMM.sh

Return type

None