nanoreactor_driver.py Command Help
Command: $SCHRODINGER/run nanoreactor_gui_dir/nanoreactor_driver.py
usage: $SCHRODINGER/run nanoreactor_gui_dir/nanoreactor_driver.py
[-h] [-charge CHARGE] [-spins UNPAIRED_ELECTRONS]
[-final_spins UNPAIRED_ELECTRONS] [-solvent SOLVENT]
[-md_time PICOSECONDS] [-meta_time PICOSECONDS] [-rmsd_save RMSD_SAVE]
[-dump FEMTOSECONDS] [-autoscale AUTOSCALE] [-kpush_scale SCALE]
[-alpha_scale SCALE] [-temp KELVIN] [-react_ident] [-TPP TPP]
[-bin_time] [-bin_energy] [-no_exhaust] [-trj] [-ts_search]
[-autots_keywords KEYWORD=VALUE KEYWORD=VALUE ...]
[-autots_jag_keywords KEYWORD=VALUE KEYWORD=VALUE ...]
[-HOST <hostname>] [-D] [-JOBNAME JOBNAME] [-taper KCAL/MOL]
[-reps REPLICATES] [-refine] [-refined_taper KCAL/MOL]
[-keywords KEYWORD=VALUE KEYWORD=VALUE ...]
input_file
Base module for the nanoreactor drivers Copyright Schrodinger, LLC. All rights
reserved.
positional arguments:
input_file Input file
options:
-h, -help Show this help message and exit.
-charge CHARGE Overall charge on the system (default: 0)
-spins UNPAIRED_ELECTRONS
Number of unpaired electrons in the initial system
(default: 0)
-final_spins UNPAIRED_ELECTRONS
Number of unpaired electrons in the final system. If
not given, the -spins value will be used (default:
None)
-solvent SOLVENT Solvent for the Poisson-Boltzmann solvent model. Must
be one of none,acetone,acetonitrile,aniline,benzaldehy
de,benzene,ch2cl2,chcl3,cs2,dioxane,dmf,dmso,ether,eth
ylacetate,furane,hexadecane,hexane,methanol,nitrometha
ne,octanol,woctanol,phenol,toluene,thf,water.
(default: none)
-md_time PICOSECONDS Picoseconds to run the relaxation MD (default: 10)
-meta_time PICOSECONDS
Picoseconds to run the Metadynamics (default: 500)
-rmsd_save RMSD_SAVE The number of reference structures associated with the
pushing (k > 0) or pulling (k < 0) strength. Default
is calculated by multiplying metadynamics simulation
time in fs with integration interval time step.
(default: None)
-dump FEMTOSECONDS Interval in femtoseconds for trajectory printout
during MD and Metadynamics simulations. (default:
None)
-autoscale AUTOSCALE Prefactor to multiply the automatically determined
sphere radius. Radius of the repulsive potential
cavity is used to confine the system. Used to avoid
spontaneous dissociation of multimolecular systems.
(default: 1.0)
-kpush_scale SCALE Scale factor for the biasing potential strength.
Higher values result in more reactions, but too high
can result in non-physical structures. Final kpush =
SCALE * 0.02 * number of atoms. (default: 1.0)
-alpha_scale SCALE Scale factor for the biasing potential width. A high
alpha results in a narrow biasing potential, meaning
that the system can escape the bias by smaller changes
to the structure. Final alpha = SCALE * 0.7. (default:
1.0)
-temp KELVIN Set the thermostat temperature for both molecular
dynamics and metadynamics run. (default: 600.15)
-react_ident Perform elementary reaction network calculation. MD
and MTD trajectories are merged and filtered based on
identical SMILES representations, (first encountered
structure for each SMILES is considered) while
preserving their full trajectory histories. Each
filtered trajectory is then subjected to sequential
xTB minimizations, progressing frame by frame until a
structure with a SMILES distinct from that of the
reactant is identified. See also flags -bin_time,
-bin_energy, and -no_exhaust. (default: False)
-TPP TPP The TPP flag is no longer supported. Use -HOST
hostname:X to indicate that X processors should be
used for the workflow. TPP will be figured
automatically. (default: 1)
-bin_time Bin structures from unoptimized trajectories by
SMILES. The structures in each bin are ordered by
increasing simulation time. Consider each structure in
each bin in order and identify the product as the
first structure for which the SMILES doesn't change
when xTB optimized. Structures with reactant SMILES
are discarded. (default: False)
-bin_energy Bin structures from unoptimized trajectories by
SMILES. The structures in each bin are ordered by
increasing unoptimized xTB energy from MD and MTD
simulation. Consider each structure in each bin in
order and identify the product as the first structure
for which the SMILES doesn't change when xTB
optimized. Structures with reactant SMILES are
discarded. (default: False)
-no_exhaust Pass this flag along with -bin_time or -bin_energy.
Only the structure at the top from each bin are
processed. i.e. structure with lowest xTB energy for
each unique SMILES in the order of appearance for
-bin_energy and first structure based on order of
increasing simulation time for -bin_time. (default:
False)
-trj If specified, write trajectory files from the MD and
Metadynamics xTB calculations and return the per-
replicate scratch directories (replicate_<n>/) to the
job launch directory for inspection. By default these
directories are removed after their contents have been
consumed. (default: False)
-ts_search If specified, perform transition state search on the
identified products from the ERN simulation. (default:
False)
-autots_keywords KEYWORD=VALUE KEYWORD=VALUE ...
If performing a transition state search for an ERN
simulation using -ts_search then specify extra AutoTS
keywords using this flag. The reactant, product,
charge, and multiplicity options for AutoTS are
handled by this script. Note this is just for AutoTS
keywords not for the Jaguar keywords used bythat
workflow which are instead specified using flag
-autots_jag_keywords. (default: None)
-autots_jag_keywords KEYWORD=VALUE KEYWORD=VALUE ...
If performing a transition state search for an ERN
simulation using -ts_search then specify Jaguar
section keywords using this flag. If not specified,
then Jaguar keywords used for energy refinement using
-keywords will be used. (default: None)
-taper KCAL/MOL Skip any product whose relaxed xTB Free energy
relative to the reactant exceeds the specified cutoff.
Use a cutoff of none to include and report all
products regardless of their relative free energy.
(default: 40)
-reps REPLICATES Number of replicate MD workflows to run (default: 8)
-refine Refine product energy using DFT (default: False)
-refined_taper KCAL/MOL
Skip any product whose refined Free energy relative to
the reactant exceeds the specified cutoff. Use a
cutoff of none to include and report all products
regardless of their relative free energy. (default:
30)
-keywords KEYWORD=VALUE KEYWORD=VALUE ...
Jaguar keywords given as a space-separated
keyword=value pairs. Any keywords given here replace
all the default keyword values. (default:
basis=LACVP** dftname=M06-L maxit=300 nofail=1)
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)
-JOBNAME JOBNAME Provide an explicit name for the job. (default: None)