prepare_for_md_driver.py Command Help
Command: $SCHRODINGER/run prepare_for_md_gui_dir/prepare_for_md_driver.py
usage: $SCHRODINGER/run prepare_for_md_gui_dir/prepare_for_md_driver.py
[-h] [-forcefield FORCE_FIELD_NAME] [-enable_metal_force_field]
[-cgffld_loc_type FORCE_FIELD_LOCATION_TYPE] [-split_components]
[-water_fftype WATER_TYPE] [-hydrogen_mass_repartition] [-monomer_ff_q]
[-ewald] [-adapt_ff] [-scale] [-ortho]
[-build_geometry_msj BUILD_GEOMETRY_MSJ] [-HOST <hostname>] [-D]
[-OPLSDIR OPLSDIR] [-JOBNAME JOBNAME]
input_file
A short driver that runs multisim on an input file to create a Desmond system
Copyright Schrodinger, LLC. All rights reserved.
positional arguments:
input_file Input file exclusively containing either atomistic or
coarse-grained structures but not both. By default
assumes atomistic structures.
options:
-h, -help Show this help message and exit.
-forcefield FORCE_FIELD_NAME
Force field to use. For atomistic systems valid force
fields are OPLS_2005, S-OPLS, SPFF,
MLFF:official:Hybrid_MPNICE,
MLFF:official:Hybrid_MPNICE_I,
MLFF:official:Hybrid_MPNICE_O,
MLFF:official:Inorganic_MPNICE,
MLFF:official:Organic_Crystals_MPNICE,
MLFF:official:Organic_Crystals_MPNICE_v1.1,
MLFF:official:Organic_MPNICE,
MLFF:official:UMA_sm_oc20, MLFF:official:UMA_sm_odac,
MLFF:official:UMA_sm_omat, MLFF:official:UMA_sm_omc
and MLFF:official:UMA_sm_omol. For coarse-grained
systems specify the name of a coarse-grained force
field (see related location type flag
-cgffld_loc_type.) (default: OPLS_2005)
-enable_metal_force_field
Use the metal force field for metal atoms. This is
only relevant if using OPLS5, and if not specified
then the standard OPLS5 force field will be used for
all atoms including metals. (default: False)
-cgffld_loc_type FORCE_FIELD_LOCATION_TYPE
Location type for a specified coarse-grained force
field. Option "installed" means from a standard
location in the Schrodinger installation while option
"local" means either from /Users/aoza/.schrodinger/mat
sci_templates/coarse_grain_force_field_parameters or
the job launch directory, i.e. the CWD. (default:
local)
-split_components Split system in components when Desmond system is
built. This can speed up the the force field
assignment for systems that contain multiple identical
molecules. (default: False)
-water_fftype WATER_TYPE
Force field type for water molecules. Must be used
with -split_components. If using "none", the Residue
Name atom property is used instead. (default: SPC)
-hydrogen_mass_repartition
Redistribute hydrogen mass to heavy atoms (default:
False)
-monomer_ff_q Use forcefield charges computed for the monomer for
the polymer. This option is particularly useful for
S-OPLS, which uses OPLS_2005 charges by default for
molecules larger than 100 heavy atoms. (default:
False)
-ewald Particle mesh Ewald (PME) method is used to compute
long-range electrostatic interactions in coarse-
grained MARTINI. (default: False)
-adapt_ff Applies structure specific modifications to the FF
after its raw application to the given structure.
(default: False)
-scale Scale the system to the density to reflect the reduced
density and cutoff values in the force field.
(default: False)
-ortho Enforce an orthorhombic PBC by zeroing out off-
diagonal elements (default: False)
-build_geometry_msj BUILD_GEOMETRY_MSJ
MSJ file containing build_geometry stage. (default:
None)
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
(default: localhost)
-D, -DEBUG Show details of Job Control operation. (default:
False)
-OPLSDIR OPLSDIR Specifies directory for custom forcefield parameters.
(default: None)
-JOBNAME JOBNAME Provide an explicit name for the job. (default: None)