autosolvate.generatetrajs.runQMMM(filename='water_solvated', spinmult=1, srun_use=False, stepsqmmmmin=250, stepsqmmmheat=1000, stepsqmmmnve=0, stepsqmmmnvt=10000, dryrun=False)[source]

Run QMMM minimization, heating and NVT trajectory run

  • filename (str, Optional, default: ‘water_solvated’) – Filename prefix for .prmtop input file and .netcdf output file

  • spinmult (int, Required) – Spin multiplicity of system

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

  • stepsqmmmmin (int, Optional, default: 250) – Number of QMMM minimization steps

  • stepsqmmmheat (int, Optional, default: 1000) – Number of QMMM heating steps

  • stepsqmmmnve (int, Optional, default: 0) – Number of QMMM NVE steps

  • stepsqmmmnvt (int, Optional, default: 10000) – Number of QMMM NVT trajectory steps

  • 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


Results stored in .netcdf files and log files

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