Synopsis

test.PhGradient [-hvV] [--scanLambdas] [--testEndStateEnergies] [--aa=<selection>] [-d=1.0e-5 Å] [--esvLambda=0.5] [--ga=ALL] [--ia=<selection>] [--pH=7.4] [--tol=1.0e-3 kcal/mol/Å] file

Description

Test the potential energy gradient for CpHMD.

Options

--esvLambda=0.5

ESV Lambda at which to test gradient.

-h, --help

Print command help and exit.

--pH, --constantPH=7.4

Constant pH value for the test.

--scanLambdas

Scan titration and tautomer lambda landscape.

--testEndStateEnergies

Test both ESV energy end states as if the polarization damping factor is initialized from the respective protonated or deprotonated state

-V, --version

Print the Force Field X version and exit.

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.

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].

Arguments

file

The atomic coordinate file in PDB format.