autosolvate.generatetrajs.runMM

autosolvate.generatetrajs.runMM(filename='water_solvated', stepsmmheat=10000, stepsmmnve=0, stepsmmnpt=300000, srun_use=False, pmemduse=False, dryrun=False, freeze_solute=False)[source]

Equilibrate with MM

Parameters:

  • filename (str, Optional, default: ‘water_solvated’) – Filename prefix for .prmtop and .inpcrd files

  • stepsmmheat (int, Optional, default: 10000) – MM heating steps

  • stepsmmnve (int, Optional, default: 0) – MM NVE steps

  • stepsmmnpt (int, Optional, default: 300000) – MM NPT steps

  • srun_use (bool, Optional, default: False) – Run all commands with a srun prefix.

  • pmemduse (bool, Optional, default: False) – Use pmemd.CUDA instead of sander

  • dryrun (bool, Optional, default: False) – Dry run mode: only generate the commands to run MD programs and save them into a file without executing the commands

Returns:

Results stored as .netcdf files and log files

Return type:

None