evaporation_driver.py Command Help
Command: $SCHRODINGER/run evaporation_gui_dir/evaporation_driver.py
usage: $SCHRODINGER/run evaporation_gui_dir/evaporation_driver.py
[-h] -solv_mol_num [SOLV_MOL_NUM ...]
[-replace_with [REPLACEMENT_MOL_NUM ...]]
[-convert [CONVERSION_MOL_NUM ...]] [-target_evap [PERCENT ...]]
[-evaps_per_iter EVAPS_PER_ITER [EVAPS_PER_ITER ...]]
[-ref_substrate REF_SUBSTRATE [REF_SUBSTRATE ...]]
[-evap_plane_height EVAP_PLANE_HEIGHT [EVAP_PLANE_HEIGHT ...]]
[-evap_radial_dist EVAP_RADIAL_DIST [EVAP_RADIAL_DIST ...]]
[-evap_com_dist EVAP_COM_DIST [EVAP_COM_DIST ...]]
[-evap_com_radial_dist EVAP_COM_RADIAL_DIST [EVAP_COM_RADIAL_DIST ...]]
[-evap_criteria EVAP_CRITERIA [EVAP_CRITERIA ...]]
[-group_type GROUP_TYPE] [-max_failed_evaps MAX_FAILED_EVAPS]
[-skip_analysis] [-skip_free_volume] [-split_components]
[-md_temp MD_TEMP] [-md_press MD_PRESS] [-md_time MD_TIME]
[-md_timestep MD_TIMESTEP] [-md_ensemble ENSEMBLE]
[-md_baro_method {MTK,Langevin,DPD}]
[-md_baro_relax_time MD_BARO_RELAX_TIME]
[-md_thermo_method {NH,Langevin,DPD}] [-md_trj_int MD_TRJ_INT]
[-md_thermo_relax_time MD_THERMO_RELAX_TIME] [-seed SEED]
[-md_umbrella] [-substrate_asl SUBSTRATE_ASL] [-force_c FORCE_C]
[-no_cms_ff_update] [-cgffld FORCE_FIELD_NAME]
[-cgffld_loc_type FORCE_FIELD_LOCATION_TYPE]
[-md_convergence MD_CONVERGENCE] [-md_max_retries MD_MAX_RETRIES]
[-rm_md_dirs] [-HOST <hostname>] [-WAIT] [-LOCAL] [-D] [-NOJOBID]
[-VIEWNAME <viewname>] [-OPLSDIR OPLSDIR] [-JOBNAME JOBNAME]
cms_file
Driver for evaporating solvents from a molecular dynamics system. This will
remove solvent molecules from a system, equilibrate via molecular dynamics,
and then repeat these two steps iteratively. Copyright Schrodinger, LLC. All
rights reserved.
positional arguments:
cms_file System containing solvent(s) to evaporate.
options:
-h, -help Show this help message and exit.
-solv_mol_num [SOLV_MOL_NUM ...]
The molecule number of one of the molecules that will
be evaporated. (default: None)
-replace_with [REPLACEMENT_MOL_NUM ...]
The molecule number of the molecules that will replace
the evaporated molecules. If specified, the
evaporating molecule will be removed from the system,
and a replacement molecule will be added at the
position of the evaporated molecule. (default: None)
-convert [CONVERSION_MOL_NUM ...]
The molecule number of the molecules that the
evaporated molecules will be converted into. This is
only applicable for converting CG molecules into
single-particle CG molecules. In this method, each
bead of the evaporating molecule will be replaced by
the specified molecule. (default: None)
-target_evap [PERCENT ...]
The percent solvent you want evaporated/removed by the
end of the simulation. This percentage is relative to
the starting amount of solvent, not the entire system.
Should be within (0, 100]. (default: None)
-evaps_per_iter EVAPS_PER_ITER [EVAPS_PER_ITER ...]
The number of molecules to remove per iteration of
evaporation. (default: None)
-ref_substrate REF_SUBSTRATE [REF_SUBSTRATE ...]
Molecule number of the reference molecule which will
be used to define evaporation zone with other flags:
-evap_criteriaand -evap_plane_height or
-evap_radial_dist or -evap_com_distor
-evap_com_radial_dist. (default: None)
-evap_plane_height EVAP_PLANE_HEIGHT [EVAP_PLANE_HEIGHT ...]
If a reference substrate is defined via the
-ref_substrate, then you may choose to create an
evaporation plane which molecules can be removed from
above or below this plane (as specified with
-evap_criteria). This flag controls the height above
the highest substrate atom at which to place the
evaporation plane.Units are in Angstroms. (default:
None)
-evap_radial_dist EVAP_RADIAL_DIST [EVAP_RADIAL_DIST ...]
The distance criteria for selecting evaporating
solvents in a radial direction, and in calculated from
the closest atom of the reference molecule. (default:
None)
-evap_com_dist EVAP_COM_DIST [EVAP_COM_DIST ...]
The distance criteria for selecting evaporating
solventsat +z/-z direction from the center of mass of
substrate. (default: None)
-evap_com_radial_dist EVAP_COM_RADIAL_DIST [EVAP_COM_RADIAL_DIST ...]
The distance criteria for selecting evaporating
solvents in radial direction from the center of mass
of substrate. (default: None)
-evap_criteria EVAP_CRITERIA [EVAP_CRITERIA ...]
Evaporation zone criteria. If a reference molecule is
defined using -ref_substrate, then you may specify if
the solvents that are `within` or `beyond` the
specified distance should be evaporated. The default
is set to `beyond`. (default: None)
-group_type GROUP_TYPE
The molecules/species in the system are identified by
this group type (default: formula)
-max_failed_evaps MAX_FAILED_EVAPS
Some settings, such as evaporation zone parameters,
may create situations where no molecules are able to
evaporate during a given evaporation iteration. This
flag sets how many times this may happen consecutively
before the entire workflow is aborted. (default: 3)
-skip_analysis Do not perform analysis calculations. (default: False)
-skip_free_volume Do not perform free volume calculations. (default:
False)
Simulation options:
-split_components Split system in components when Desmond system is
built. This can speed up the the force field
assignment for systems that contain multiple identical
molecules. (default: False)
-md_temp MD_TEMP Temperature (in K) of the simulations. (default:
300.0)
-md_press MD_PRESS Pressure (in bar) of the simulations. (default:
1.01325)
-md_time MD_TIME MD time (in ns) of the simulation. (default: 100.0)
-md_timestep MD_TIMESTEP
MD time step (in fs) of the simulations. (default:
2.0)
-md_ensemble ENSEMBLE
Desmond ensemble. Known values are: NVE, NVT, NPT
(default: NPT)
-md_baro_method {MTK,Langevin,DPD}
NPT ensemble method. Known values are Martyna-Tobias-
Klein, Langevin, DPD (default: MTK)
-md_baro_relax_time MD_BARO_RELAX_TIME
Barostat damping constant. (default: 1.2)
-md_thermo_method {NH,Langevin,DPD}
NVT ensemble method. Known values are Nose-Hoover
chain, Langevin, DPD (default: NH)
-md_trj_int MD_TRJ_INT
MD trajectory recording interval (in ps). (default:
10.0)
-md_thermo_relax_time MD_THERMO_RELAX_TIME
Thermostat damping constant. (default: 1.2)
-seed SEED Seed for random number generator. (default: 1234)
-md_umbrella Run desmond subjobs on the driver host. (default:
False)
-substrate_asl SUBSTRATE_ASL
ASL for the substrate to apply positional restraints.
(default: None)
-force_c FORCE_C Force constant (kcal mol-1 Å-2) to use for the
substrate positional restraints. (default: None)
-no_cms_ff_update Do not update the force field of an input CMS file to
the current version. (default: False)
-cgffld FORCE_FIELD_NAME
Name of coarse-grained force field to use. See related
location type flag -cgffld_loc_type. (default: None)
-cgffld_loc_type FORCE_FIELD_LOCATION_TYPE
Location type for the force field specified with
-cgffld. Option installed means from a standard
location in the Schrodinger installation, while option
local means either from /Users/bozhang/.schrodinger/ma
tsci_templates/coarse_grain_force_field_parameters or
the job launch directory, i.e. the CWD. (default:
local)
-md_convergence MD_CONVERGENCE
Convergence criteria for equilibration simulations,
defined as percentage change in density of system
during the equilibration stage. (default: 5)
-md_max_retries MD_MAX_RETRIES
Maximum iterations to run equilibrium simulation to
achieve convergence. Setting this to 1 (default)
disables the convergence check during equilibration.
(default: 1)
-rm_md_dirs By default, all job files for all equilibration steps
will be saved in sub-directories named according to
the evaporation step. Use this option to remove these
sub-directories. Note that using this option will
prevent you from being able to view trajectories in
Maestro. (default: False)
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
(default: localhost)
-WAIT Do not return a prompt until the job completes.
(default: False)
-LOCAL Do not use a temporary directory for job files. Keep
files in the current directory. (default: False)
-D, -DEBUG Show details of Job Control operation. (default:
False)
-NOJOBID Run the job directly, without Job Control layer.
(default: False)
-VIEWNAME <viewname> Specifies viewname used in job filtering in maestro.
(default: False)
-OPLSDIR OPLSDIR Specifies directory for custom forcefield parameters.
(default: None)
-JOBNAME JOBNAME Provide an explicit name for the job. (default: None)