diffusion_coefficient_msd_driver.py Command Help
Command: $SCHRODINGER/run diffusion_coefficient_gui_dir/diffusion_coefficient_msd_driver.py
usage: $SCHRODINGER/run diffusion_coefficient_gui_dir/diffusion_coefficient_msd_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}]
[-trj_folder TRJ_FOLDER] [-data_start DATA_NUMBER]
[-trj_frame_num TRJ_NUMBER] [-variation VARIATION] [-run_type RUN_TYPE]
[-tau_start NANOSECOND] [-tau_end NANOSECOND] [-md_sim_num MD_SIM_NUM]
[-search_inputs] [-no_cms_ff_update] [-asl ASL] [-com_type COM_TYPE]
[-smarts SMARTS] [-ref ASL] [-momentum] [-plane X,Y,Z] [-axis] [-vel]
[-ionic_method IONIC_METHOD]
[-block_avg_win_interval BLOCK_AVG_WIN_INTERVAL]
[-block_avg_win_size BLOCK_AVG_WIN_SIZE]
[-ms_win_interval MS_WIN_INTERVAL] [-ms_win_size MS_WIN_SIZE]
[-num_trace NUM_TRACE]
[-diffusion_methods DIFFUSION_METHODS [DIFFUSION_METHODS ...]]
[-use_ctname_smiles] [-enegrp_temperature ENEGRP_TEMPERATURE]
[-HOST <hostname>] [-WAIT] [-LOCAL] [-D] [-NOJOBID]
[-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)
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: NVE)
-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)
-no_cms_ff_update Do not update the force field of an input CMS file to
the current version. (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: 1.0)
-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)
-trj_folder TRJ_FOLDER
Analyze this trajectory, if -run_type post (default:
None)
Analysis Parameter:
-data_start DATA_NUMBER
DATA_NUMBER at the beginning of a molecular dynamics
data will be excluded from analysis. (default: 10)
-trj_frame_num TRJ_NUMBER
Read this number of trajectory frames or until the
end. (default: None)
-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:
0.1)
-tau_start NANOSECOND
Msd data before MD_TAU_START (ns) are excluded for
diffusion coefficient calculation. (default: 0.01)
-tau_end NANOSECOND Msd data after MD_TAU_END (ns) are excluded for
diffusion coefficient calculation. (default: 0.99)
-asl ASL ASL string to define atom selections. (default: all)
-com_type COM_TYPE Use Center of Mass (COM) of each COM_TYPE
(atom|molecule|monomer|SMARTS). (default: molecule)
-smarts SMARTS Use SMARTS pattern to define the center of mass for
diffusion coefficient calculation, if -com_type
SMARTS. (default: None)
-ref ASL ASL string to define atom selection for computing the
mass center. (default: None)
-momentum The mass center of the reference atoms is forced to
stay at the same position. If the mass center of
reference atoms has certain displacement between
original trajectory frames (translation), all the
atoms in the -sel group will be shifted by that
displacement to cancel the translation effect on
trajectories. (default: False)
-plane X,Y,Z The anisotropic diffusion coefficient along this
direction and in the perpendicular plane are
calculated. (e.g., 0,0,1) (default: None)
-axis The anisotropic diffusion coefficient along all-three
directions. (default: False)
-vel Use velocity information to help adjust system
translation. (default: False)
-ionic_method IONIC_METHOD
Method to compute Stefan-Maxwell diffusivities.
(default: None)
-block_avg_win_interval BLOCK_AVG_WIN_INTERVAL
Time window interval (in ns) to perform block
averaging (default: None)
-block_avg_win_size BLOCK_AVG_WIN_SIZE
Time window size (in ns) to perform block averaging
(default: None)
-ms_win_interval MS_WIN_INTERVAL
Time window interval (in ns) to perform Stefan-Maxwell
diffusion coefficient calculation (default: 0.01)
-ms_win_size MS_WIN_SIZE
Time window size (in ns) to perform Stefan-Maxwell
diffusion coefficient calculation (default: 1.0)
-num_trace NUM_TRACE The number of mass centers to export trajectory trace
for. If 0, no trajectory trace will be exported.
(default: 10)
-diffusion_methods DIFFUSION_METHODS [DIFFUSION_METHODS ...]
Method to compute diffusion coefficient. (default:
['self_diffusion'])
-use_ctname_smiles Use the smiles string of the molecule to define
component name in onsager coefficient calculation.
(default: False)
-enegrp_temperature ENEGRP_TEMPERATURE
Temperature (K) for viscosity calculation, if
molecular dynamics simulation is skipped. (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: 1)
-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)
-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)
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)