deposition_driver2.py Command Help
Command: $SCHRODINGER/run deposition_gui_dir/deposition_driver2.py
usage: $SCHRODINGER/run deposition_gui_dir/deposition_driver2.py
[-h] [-iterations ITERATIONS] [-idealize_me_envir]
[-initial_atomic_velocity INITIAL_ATOMIC_VELOCITY]
[-brownie_time BROWNIE_TIME] [-md_time MD_TIME]
[-md_timestep MD_TIMESTEP] [-md_trj_int MD_TRJ_INT] [-md_temp MD_TEMP]
[-md_ensemble ENSEMBLE] [-save_trj_data {none,cms,trj}] [-seed SEED]
[-md_umbrella] [-substrate_asl SUBSTRATE_ASL] [-force_c FORCE_C]
[-no_cms_ff_update] [-velocity_temp TEMPERATURE [TEMPERATURE ...]]
[-velocity_min VELOCITY_MIN [VELOCITY_MIN ...]] [-use_input_vel]
[-disable_rotations] [-md_ensemble2 ENSEMBLE] [-md_time2 MD_TIME2]
[-md_temp2 MD_TEMP2] -adsorbate ADSORBATE [ADSORBATE ...] -composition
COMPOSITION [COMPOSITION ...] -rate RATE [RATE ...] -nadsorbates
NADSORBATES [NADSORBATES ...] [-st2_file ST2_FILE]
[-energy_avg ENERGY_AVG] [-delete_cutoff DELETE_CUTOFF]
[-one_md_per_iteration] [-clean_under] [-non_periodic]
[-msj_file MSJ_FILE] [-D] [-OPLSDIR OPLSDIR]
icms
Driver to perform molecular deposition. Copyright Schrodinger, LLC. All rights
reserved.
positional arguments:
icms Input desmond CMS file.
options:
-h, -help Show this help message and exit.
-iterations ITERATIONS
Number of iterations to run (default: 30)
-idealize_me_envir Idealize metal environment in the input geometry.
(default: False)
-initial_atomic_velocity INITIAL_ATOMIC_VELOCITY
Initial atomic velocity component (A/ps) along the
interface normal towards substrate. (default: None)
-brownie_time BROWNIE_TIME
Include Brownian Minimization stage before simulation.
(default: None)
-md_time MD_TIME MD time (in ns) of the simulation. (default: 200.0)
-md_timestep MD_TIMESTEP
MD time step (in fs) of the simulations. (default:
2.0)
-md_trj_int MD_TRJ_INT
MD trajectory recording interval (in ps). (default:
10.0)
-md_temp MD_TEMP Temperature (in K) of the simulations. (default:
300.0)
-md_ensemble ENSEMBLE
Desmond ensemble. Known values are: NVE, NVT, NPT
(default: NVT)
-save_trj_data {none,cms,trj}
Specify whether intermediate CMS or trajectory files
be included with the job output. Choices are none
(save no files), cms (save .cms files) and trj (save
.cms and trajectory files). Default is none. (default:
none)
-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: 10000.0)
-no_cms_ff_update Do not update the force field of an input CMS file to
the current version. (default: False)
-velocity_temp TEMPERATURE [TEMPERATURE ...]
Temperature of the deposition along the C-axis.
Initial velocity will be obtained from this value.
(default: None)
-velocity_min VELOCITY_MIN [VELOCITY_MIN ...]
Minimum velocity (A/ps). This value will be added to
the velocity obtained from temperature. (default:
None)
-use_input_vel Use input velocities (if present). Z velocity value
will added to any requested value using -velocity_min,
-velocity_temp or -initial_atomic_velocity. (default:
False)
-disable_rotations Do not rotate adsorbate molecule when placing in the
cell. (default: False)
-md_ensemble2 ENSEMBLE
Desmond ensemble for the optional post deposition
stage. Known values are: NVE, NVT, NPT (default: NVT)
-md_time2 MD_TIME2 MD time (in ps) for the optional post deposition
stage. (default: 0)
-md_temp2 MD_TEMP2 Temperature (in K) for the optional post deposition
stage. (default: 300.0)
-adsorbate ADSORBATE [ADSORBATE ...]
Adsorbate file. (default: None)
-composition COMPOSITION [COMPOSITION ...]
Number of molecules deposited per iteration (default:
None)
-rate RATE [RATE ...]
Rate of deposition (deposit every n-th iteration)
(default: None)
-nadsorbates NADSORBATES [NADSORBATES ...]
Number of adsorbates deposited at once. (default:
None)
-st2_file ST2_FILE Analysis input file. Run after each iteration
(default: None)
-energy_avg ENERGY_AVG
Percent to use when computing interaction energies.
(default: 20.0)
-delete_cutoff DELETE_CUTOFF
Cutoff distance (A) for which molecule is considered
not adsorbed after the MD run and deleted. (default:
None)
-one_md_per_iteration
Group deposition steps, such that only one MD
simulation is run for all deposited adsorbates each
iteration. (default: False)
-clean_under Remove adsorbates that end up "under" the substrate.
(default: False)
-non_periodic Use non-periodic MD. Non-periodicity is achieved by
applying repulsive wall at the edge of MD system.
(default: False)
-msj_file MSJ_FILE MSJ input file, will be used instead of all the MD
flags. (default: None)
Job Control Options:
-D, -DEBUG Show details of Job Control operation. (default:
False)
-OPLSDIR OPLSDIR Specifies directory for custom forcefield parameters.
(default: None)