thermophysical_properties_driver.py Command Help
Command: $SCHRODINGER/run thermophysical_properties_gui_dir/thermophysical_properties_driver.py
usage: $SCHRODINGER/run thermophysical_properties_gui_dir/thermophysical_properties_driver.py
[-h] -icms ICMS -min_temp MIN_TEMP [-max_temp MAX_TEMP]
[-temp_step TEMP_STEP] [-density_stage_time DENSITY_STAGE_TIME]
[-density_convergence DENSITY_CONVERGENCE]
[-max_convergence_retries MAX_CONVERGENCE_RETRIES]
[-job_order {simultaneous,max_first,min_first}]
[-ht_timestep FEMTOSECONDS] [-ht_temp KELVIN]
[-frame_interval PICOSECONDS] [-load_temp_structure KELVIN]
[-run_relaxation] [-lcte] [-max_deltap MAX_DELTAP] [-md_press MD_PRESS]
[-save_ene] [-md_mlff_time MD_MLFF_TIME]
[-md_mlff_timestep MD_MLFF_TIMESTEP] [-seed SEED]
[-md_timestep MD_TIMESTEP] [-md_enegrp_int MD_ENEGRP_INT]
[-save_trj_data {none,cms,trj}] [-combine_trj] [-md_umbrella]
[-md_eneseq_int MD_ENESEQ_INT] [-md_isotropy ISOTROPY_POLICY]
[-no_cms_ff_update] [-md_mlff MLFF_FORCE_FIELD] [-gpu]
[-HOST <hostname>] [-WAIT] [-LOCAL] [-D] [-NOJOBID]
[-VIEWNAME <viewname>] [-OPLSDIR OPLSDIR] [-JOBNAME JOBNAME]
options:
-h, -help Show this help message and exit.
-icms ICMS Disordered system to run Desmond MD simulations on.
(default: None)
-min_temp MIN_TEMP Minimum temp (K) to run MD simulation at. (default:
None)
-max_temp MAX_TEMP Maximum temp (K) to run MD simulation at. (default:
None)
-temp_step TEMP_STEP Temperature step size (K) to run simulations at
between min_temp and max_temp. (default: None)
-density_stage_time DENSITY_STAGE_TIME
Simulation time (ns) to set the MD density stage to.
(default: 60.0)
-density_convergence DENSITY_CONVERGENCE
Threshold for considering a density to be converged.
Calculated as 100 * (Std deviation / Average) over the
final 20 percent of a density Desmond MD simulation.
(default: 5.0)
-max_convergence_retries MAX_CONVERGENCE_RETRIES
The maximum number of times to rerun the density
protocol for each temperature to achieve density
convergence. (default: 1)
-job_order {simultaneous,max_first,min_first}
Order in which to run the MD density protocol
simulations. (default: simultaneous)
-ht_timestep FEMTOSECONDS
The timestep in femtoseconds to use for temperatures
above that given by the -ht_temp flag. The default is
to use 2.0 fs timesteps for all temperatures.
(default: None)
-ht_temp KELVIN The temperature above which the value of -ht_timestep
should be used as the MD timestep. Without
-ht_timestep, this flag is ignored. (default: 700.0)
-frame_interval PICOSECONDS
Amount of simulation time between writing trajectory
frames. (default: 600.0)
-load_temp_structure KELVIN
Load converged structure closest to temp (K).
(default: None)
-run_relaxation run the relaxation protocol on the input system before
running density simulations. (default: False)
-lcte Compute Linear coefficient of expansion (default:
False)
-max_deltap MAX_DELTAP
Stop simulation if change is density exceeds threshold
value (default: None)
-md_press MD_PRESS Pressure (in bar) of the simulations. (default:
1.01325)
-save_ene Save .ene file. (default: False)
-md_mlff_time MD_MLFF_TIME
Simulation time (ns) for MLFF density stage. (default:
1.0)
-md_mlff_timestep MD_MLFF_TIMESTEP
Timestep (fs) for MLFF simulation. (default: 0.5)
-seed SEED Seed for random number generator. (default: 1234)
-md_timestep MD_TIMESTEP
MD time step (in fs) of the simulations. (default:
2.0)
-md_enegrp_int MD_ENEGRP_INT
MD energy group recording interval (in ps). (default:
10.0)
-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)
-combine_trj Merge all trajectories into a single one. (default:
False)
-md_umbrella Run desmond subjobs on the driver host. (default:
False)
-md_eneseq_int MD_ENESEQ_INT
MD energy recording interval (in ps). (default: 10.0)
-md_isotropy ISOTROPY_POLICY
Desmond barostat isotropy policy. Known values are:
isotropic, semi_isotropic, constant_axis_a,
constant_axis_b, constant_axis_c, anisotropic,
flexible (default: isotropic)
-no_cms_ff_update Do not update the force field of an input CMS file to
the current version. (default: False)
-md_mlff MLFF_FORCE_FIELD
Machine learning force field to use. {'Hybrid_MPNICE':
'Hybrid_MPNICE', 'Hybrid_MPNICE_I': 'Hybrid_MPNICE_I',
'Hybrid_MPNICE_O': 'Hybrid_MPNICE_O',
'Inorganic_MPNICE': 'Inorganic_MPNICE',
'Organic_Crystals_MPNICE': 'Organic_Crystals_MPNICE',
'Organic_MPNICE': 'Organic_MPNICE'} (default: None)
-gpu No longer used. All simulations will run on GPU
regardless of this flag. (default: True)
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)