Synopsis

test.OSTGradient [-hvV] [--meta] [--aa=<selection>] [--ac=<selection>] [--acRes=<selection>] [-d=1.0e-5 Å] [--ga=ALL] [--ia=<selection>] [-l=-1] [--tol=1.0e-3 kcal/mol/Å] [--uc=<selection>] file

Description

OSTGradient script tests the Orthogonal Space Tempering Potential.

Options

-h, --help

Print command help and exit.

--meta, --metaDynamics

Use a 1D metadynamics style bias.

-V, --version

Print the Force Field X version and exit.

Atom Selection Options

--aa, --active=<selection>

Ranges of active atoms [NONE, ALL, Range(s): 1-3,6-N].

--ia, --inactive=<selection>

Ranges of inactive atoms [NONE, ALL, Range(s): 1-3,6-N].

Gradient Options

-d, --dx=1.0e-5 Å

Finite-difference step size.

--ga, --gradientAtoms=ALL

Ranges of degrees of freedom to test [ALL, NONE, Range(s): 1-3,6-N].

--tol, --tolerance=1.0e-3 kcal/mol/Å

Gradient error tolerance.

-v, --verbose

Print out the energy for each step.

Alchemical Options

--ac, --alchemicalAtoms=<selection>

Specify alchemical atoms [ALL, NONE, Range(s): 1-3,6-N].

--acRes, --alchemicalResidues=<selection>

Specify alchemical residues by chain and residue number [A4,B21]

-l, --lambda=-1

Initial lambda value.

--uc, --unchargedAtoms=<selection>

Specify atoms without electrostatics [ALL, NONE, Range(s): 1-3,6-N].

Arguments

file

XYZ or PDB input file.