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.