autosolvate.clustergen.clustergen

autosolvate.clustergen.clustergen(filename='water_solvated.prmtop', trajname='water_solvated-qmmmnvt.netcdf', startframe=0, interval=100, size=4, srun_use=False, spherical=False)[source]

Extract microsolvated cluster around center solute

Parameters:

  • filename (str, default: ‘water_solvated.prmtop’) – Filename name of .prmtop files

  • trajname (str, default: ‘water_solvated-qmmmnvt.netcdf’) – Name of trajectory

  • startframe (int, Optional, default: 0) – First frame to extract the microsolvated clusters from trajectory

  • interval (int, Optional, default: 100) – Interval at which to extract microsolvated clusters from trajectory

  • size (float, Optional, default: 4) – size of solvent shell around center solute in Angstrom

  • spherical (bool, Optional, default: False:) – switches from default aspherical solvent shell to spherical solvent shell, solvent shell size is not measured from center of mass

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

Returns:

Result stored as ‘filename’-cluster.xyz file

Return type:

None