Force Field Xtest.LambdaGradient(1)
Synopsis
test.LambdaGradient [-hvV] [--ls] [--sdX] [--sk2] [--ac=<selection>] [--ac2=<selection>] [--acRes=<selection>] [--acRes2=<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…
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].
- --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].
Coordinate 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].
- --acRes2, --alchemicalResidues2=<selection>
- Specify alchemical residues by chain and residue number for the 2nd topology [A4,B21]
- --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].