diffusion_coefficient_gk_driver.py Command Help
Command: $SCHRODINGER/run diffusion_coefficient_gui_dir/diffusion_coefficient_gk_driver.py
usage: $SCHRODINGER/run diffusion_coefficient_gui_dir/diffusion_coefficient_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] [-md_save_trj]
[-trj_folder TRJ_FOLDER] [-data_start DATA_NUMBER] [-asl ASL]
[-trj_frame_num TRJ_NUMBER] [-block_num BLOCK_NUM]
[-variation VARIATION] [-run_type RUN_TYPE] [-tau_start NANOSECOND]
[-tau_end NANOSECOND] [-no_cms_ff_update] [-prm] [-max_ram MB]
[-diffusion_methods DIFFUSION_METHODS [DIFFUSION_METHODS ...]]
[-md_remove_constraint] [-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_CMS
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_CMS Desmond cms for molecular dynamics simulations
-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: 100.0)
-md_timestep MD_TIMESTEP
MD time step (in fs) of the simulations. (default:
2.0)
-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_remove_constraint
Any bond, angle and other user-defined restraints will
be removed during MD simulation, if True. (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)
-md_save_trj Save the trajectory from the molecular dynamics
simulation. (default: False)
-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)
-asl ASL ASL string to define atom selection. (default: all)
-trj_frame_num TRJ_NUMBER
Read this number of trajectory frames or until the
end. (default: None)
-block_num BLOCK_NUM Data from original single simulation will be divided
into BLOCK_NUM short successive blocks, and each block
will be analyzed independently to calculate standard
deviation for coefficient of variation check (default:
1)
-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
Msd data before MD_TAU_START (ns) are excluded for
diffusion coefficient and vibrational power spectrum
calculation. (default: 0.01)
-tau_end NANOSECOND Msd data after MD_TAU_END (ns) are excluded for
diffusion coefficient and vibrational power spectrum
calculation. (default: 10000.0)
-prm Calculate vibrational power spectrum for atoms
selected by -asl. (default: False)
-max_ram MB MAX_RAM (MB) is the largerst allowable memory usage.
If the analysis uses more that MAX_RAM (MB) memory,
the job will be aborted. (default: 4000)
-diffusion_methods DIFFUSION_METHODS [DIFFUSION_METHODS ...]
Method to compute diffusion coefficient. (default:
['self_diffusion'])
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)