polymer_chain_analysis_driver.py Command Help
Command: $SCHRODINGER/run polymer_chain_analysis_gui_dir/polymer_chain_analysis_driver.py
usage: $SCHRODINGER/run polymer_chain_analysis_gui_dir/polymer_chain_analysis_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] [-run_type RUN_TYPE] [-cal_method METHOD]
[-sample_mol SAMPLE MOL] [-extended_chain_length ANGSTROM]
[-radius_of_gyration] [-rg_tensor] [-order_parameter] [-polymer_chain]
[-all_trans] [-end_to_internal N_TO_SKIP] [-HOST <hostname>] [-WAIT]
[-LOCAL] [-D] [-NOJOBID] [-VIEWNAME <viewname>] [-JOBNAME JOBNAME]
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)
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)
-cal_method METHOD Use end_to_end to calculate persistence length.
(default: None)
-sample_mol SAMPLE MOL
A molecule number to select all molecules of the same
type (default: None)
-extended_chain_length ANGSTROM
Use this length as the extended chain length in worm-
like chain model. (default: None)
-radius_of_gyration Calculate the Radius of gyration for each molecule
matching the sample molecule (-sample_mol). If a
sample molecule number is not provided, calculate for
the molecules included by ASL string (-asl). (default:
False)
-rg_tensor Calculate the diagonal elements of diagonalized radius
of gyration tensor for each molecule in Angstrom^2,
matching the sample molecule (-sample_mol). If a
sample molecule number is not provided, calculate for
the molecules included by ASL string (-asl). (default:
False)
-order_parameter Calculate the order parameter of the principal axes
for eachmolecule matching the sample molecule
(-sample_mol). If a sample molecule number is not
provided then calculate for the molecules included by
ASL string (-asl). (default: False)
-polymer_chain If False, the two end atoms in the longest bond path
for each selected molecule are used as the two ends.
If True, find the unique pair of initiator and
terminator in each selected molecules and use them as
the molecule two ends. If one selected molecule has
zero or more than one possible of INI / TRM pairs, the
calculation will fail. (default: False)
-all_trans Use the length of all-trans conformer as the extended
chain length. (default: False)
-end_to_internal N_TO_SKIP
Calculate internal distances for every Nth atom in the
backbonebackbone. If given, calculate the internal
distances between backbone atoms separated by
N_TO_SKIP bonds. If N_TO_SKIP is larger than number of
backbone atoms, N_TO_SKIP is set as 1. (default: None)
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)
-JOBNAME JOBNAME Provide an explicit name for the job. (default: None)