Test potential energy derivatives with respect to Lambda.
test.LambdaGradient(1) Manual Page
Name
test.LambdaGradient - Test potential energy derivatives with respect to Lambda.
Synopsis
test.LambdaGradient [-hvvV] [--ls] [--sdX] [--sk2] [--ac=<selection>] [--ac=<selection>] [--ac2=<selection>] [--ac2=<selection>] [-d=1.0e-5 Å] [-d=1.0e-5 Å] [--ga=ALL] [--ga=ALL] [-l=-1] [-l=-1] [--lm=0.01] [--np=1] [--np=1] [--sf=1.0] [--sf=1.0] [--tol=1.0e-3 kcal/mol/Å] [--tol=1.0e-3 kcal/mol/Å] [--uaA=-1] [--uaA=-1] [--uaB=-1] [--uaB=-1] [--uc=<selection>] [--uc=<selection>] [--uc2=<selection>] [--uc2=<selection>] files…
Description
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 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 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.