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