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test.LambdaGradient(1) Manual Page

Name

test.LambdaGradient - Test potential energy derivatives with respect to Lambda.

Synopsis

test.LambdaGradient [-hvV] [--ls] [--sdX] [--sk2] [--ac=<selection>] [--ac2=<selection>] [-d=1.0e-5 Å] [--ga=ALL] [-l=-1] [--lm=0.01] [--np=1] [--sf=1.0] [--tol=1.0e-3 kcal/mol/Å] [--uaA=-1] [--uaB=-1] [--uc=<selection>] [--uc2=<selection>] files…​

Description

Test potential energy derivatives with respect to Lambda.

Options

-h, --help

Print command help and exit.

--lm, --lambdaMoveSize=0.01

Size of the lambda moves during the test.

--ls, --lambdaScan

Scan lambda values.

--sdX, --skipdX

Skip calculating per-atom dUdX values and only test lambda gradients.

--sk2, --skip2

Skip 2nd derivatives.

-V, --version

Print the Force Field X version and exit.

Alchemical Options

--ac, --alchemicalAtoms=<selection>

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

-l, --lambda=-1

Initial lambda value.

--uc, --unchargedAtoms=<selection>

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

Gradient Options

-d, --dx=1.0e-5 Å

Finite-difference step size.

--ga, --gradientAtoms=ALL

Ranges of atoms 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 for Dual and Quad Topologies

--ac2, --alchemicalAtoms2=<selection>

Specify alchemical atoms for the 2nd topology [ALL, NONE, Range(s): 1-3,6-N].

--np, --nParallel=1

Number of topologies to evaluate in parallel

--sf, --switchingFunction=1.0

Switching function to use for dual topology: options are TRIG, MULT, or a number (original behavior with specified lambda exponent)

--uaA, --unsharedA=-1

Unshared atoms in the A dual topology (e.g. 1-24.32-65).

--uaB, --unsharedB=-1

Unshared atoms in the B dual topology (e.g. 1-24.32-65).

--uc2, --unchargedAtoms2=<selection>

Specify atoms without electrostatics for the 2nd topology [ALL, NONE, Range(s): 1-3,6-N].

Arguments

files…​

The atomic coordinate files in PDB or XYZ format.