viscosity_gk_driver.py Command Help
Command: $SCHRODINGER/run viscosity_gui_dir/viscosity_gk_driver.py
usage: $SCHRODINGER/run viscosity_gui_dir/viscosity_gk_driver.py
[-h] [-md_ensemble MD_ENSEMBLE] [-md_temp MD_TEMP] [-md_press MD_PRESS]
[-md_time MD_TIME] [-md_timestep MD_TIMESTEP] [-md_umbrella]
[-seed SEED] [-md_trj_int PICOSECONDS] [-save_trj_data {none,cms,trj}]
[-data_last_frac FRACTION] [-variation VARIATION] [-run_type RUN_TYPE]
[-tau_start NANOSECOND] [-tau_end NANOSECOND] [-md_sim_num MD_SIM_NUM]
[-search_inputs] [-md_thermo_method {NH,Langevin,DPD}]
[-md_thermo_relax_time MD_THERMO_RELAX_TIME] [-no_cms_ff_update]
[-save_mode {minimum,standard,verbose}] [-use_localhost_gpu]
[-press_dat PRESS_DAT [PRESS_DAT ...]] [-md_enegrp_int PICOSECONDS]
[-md_remove_constraint] [-md_enegrp_start PICOSECONDS] [-method METHOD]
[-diffusion DIFFUSION_OPTIONS] [-msd_viscosity MSD_VISCOSITY_OPTIONS]
[-eh_viscosity EH_VISCOSITY_OPTIONS]
[-enegrp_temperature ENEGRP_TEMPERATURE]
[-traj_dat TRAJ_DAT [TRAJ_DAT ...]] [-viscosity_file VISOCITY_FILE]
[-shear_viscosity_csv SHEAR_VISCOSITY_OUTPUTS]
[-fitting_method FITTING_METHOD] [-average_period AVERAGE_PERIOD]
[-zip_outputs] [-slice_intvl SLICE_INTVL] [-HOST <hostname>] [-WAIT]
[-D] [-VIEWNAME <viewname>] [-OPLSDIR OPLSDIR] [-JOBNAME JOBNAME]
[-SUBHOST <hostname> or -SUBHOST <hostname:nproc> or -SUBHOST "hostname1:nproc1 ... hostnameN:nprocN"]
INPUT_FILE
options:
-h, -help Show this help message and exit.
-run_type RUN_TYPE Define the type of this calculation. full: run
molecular dynamics simulations and post analysis;
post: skip the molecular dynamics simulations and
perform post-analysis; multi: post-analysis only
includes multi-run average and curve fitting; fit:
only perform curve fitting on the averaged data.
(default: full)
-save_mode {minimum,standard,verbose}
minimum saves only the minimum files for the viewer;
standard saves standard files from desmond simulations
in addition; verbose saves all intermediate files.
(default: None)
-use_localhost_gpu If available, use the driver's localhost GPU for MD
simulations. (default: False)
MD Basic Setting:
INPUT_FILE Desmond cms for molecular dynamics simulations or
Maestro mae for post analysis.
-md_ensemble MD_ENSEMBLE
Molecular dynamics ensemble (NVE, NVT, NPT) for data
collection. (default: NVT)
-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: 1.0)
-md_timestep MD_TIMESTEP
MD time step (in fs) of the simulations. (default:
1.0)
-md_umbrella Run desmond subjobs on the driver host. (default:
False)
-seed SEED Seed for random number generator. (default: 1234)
-md_thermo_method {NH,Langevin,DPD}
NVT ensemble method. Known values are Nose-Hoover
chain, Langevin, DPD (default: NH)
-md_thermo_relax_time MD_THERMO_RELAX_TIME
Thermostat damping constant. (default: 1.2)
-no_cms_ff_update Do not update the force field of an input CMS file to
the current version. (default: False)
-md_remove_constraint
Any bond, angle and other user-defined constraints
(Shake) will be removed during MD simulation.
(default: False)
MD Output Setting:
-md_trj_int PICOSECONDS
Trajectories will be recorded every FLAG_MD_TRJ_INT
(ps) during the molecular dynamics simulations.
(default: 20.0)
-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)
-press_dat PRESS_DAT [PRESS_DAT ...]
Please provide either an energy group / ptensor file
or a machine learning log file with pressure tensor
recorded if molecular dynamics simulations are
skipped. (default: None)
-md_enegrp_int PICOSECONDS
Pressure tensor will be recorded every this ps during
the molecular dynamics simulations. (default: 0.01)
-md_enegrp_start PICOSECONDS
Start to record pressure tensor when simulation time
this ps. (default: 0.0)
-traj_dat TRAJ_DAT [TRAJ_DAT ...]
Trajectory to get volume if molecular dynamics
simulation is skipped. (default: None)
Analysis Parameter:
-data_last_frac FRACTION
The last this fraction of the molecular dynamics data
will be used for analysis. (default: 0.8)
-variation VARIATION If provided, the tau_end is adjusted according to
VARIATION (standard deviation over mean) so that Tau
region has variation less than VARIATION. (default:
None)
-tau_start NANOSECOND
Pressure tensor data before MD_TAU_START (ns) are
excluded for shear viscosity calculation. (default:
0.002)
-tau_end NANOSECOND Pressure tensor data after MD_TAU_END (ns) are
excluded for shear viscosity calculation. (default:
0.99)
-method METHOD GK calculates the autocorrelation of pressure tensors
and then do integration to compute the viscosity; MSD
integrates the pressure tensors and then calculate
mean squared displacement to compute the viscosity
(default: GK)
-diffusion DIFFUSION_OPTIONS
Diffusion options for post analysis. (default: None)
-msd_viscosity MSD_VISCOSITY_OPTIONS
Viscosity options using MSD method (default: None)
-eh_viscosity EH_VISCOSITY_OPTIONS
Viscosity options using Einstein-Helfand method
(default: None)
-enegrp_temperature ENEGRP_TEMPERATURE
Temperature (K) for viscosity calculation, if
molecular dynamics simulation is skipped. (default:
None)
-viscosity_file VISOCITY_FILE
The viscosity output file of one single calculation.
(default: None)
-shear_viscosity_csv SHEAR_VISCOSITY_OUTPUTS
The shear viscosity csv file over multiple
calculations. (use with -run_type fit) (default: None)
-fitting_method FITTING_METHOD
average to get the mean viscosity over certain tau
range; exponential to fit a exponential function.
(default: None)
-average_period AVERAGE_PERIOD
The mean of every AVERAGE_PERIOD pressure tensors is
calculated, and these pre-averaged tensors are used
for further calculation. (default: 1)
-zip_outputs The registered output files of each molecular dynamics
simulation with the following analysis is zipped to
reduced to file size. (default: False)
-slice_intvl SLICE_INTVL
The viscosity function is sliced by this interval and
saved to the disk. (default: None)
Independent Run:
-md_sim_num MD_SIM_NUM
MD_SIM_NUM numbers of independent molecular dynamics
simulations each followed by post-analysis are fired
off under jobcontrol. (default: 10)
-search_inputs When -run_type post or -run_type multi, this flag
allows users to search the folder containing the user-
defined file so that multiple files with the same
extension from previous molecular dynamics simulations
or post-analyses are used as inputs for this
calculation. (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)
-D, -DEBUG Show details of Job Control operation. (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)
Standard Options:
-SUBHOST <hostname> or -SUBHOST <hostname:nproc> or -SUBHOST "hostname1:nproc1 ... hostnameN:nprocN"
Run the subjobs on the specified hosts. The driver is
run on the host specified with -HOST. (default: None)