Test Lambda Derivatives
Test the potential energy gradient using finite-differences.
Usage: ffxc test.LambdaGradient [-hv] [--ls] [--sdX] [--sk2] [--af=-1] [--as=1] [--ef1=-1] [--ef2=-1] [--es1=1] [--es2=1] [--f1=-1] [--f2=-1] [--la=-1] [--la1=-1] [--la2=-1] [--lm=0.01] [--np=1] [--s1=0] [--s2=0] [--sf=1.0] [--tol=1.0e-3] [--uaA=-1] [--uaB=-1] [-a=1] [-d=1.0e-5] [-l=-1] files...
Test potential energy derivatives with respect to Lambda.
files... The atomic coordinate file in PDB or XYZ format.
--af, --activeFinal=-1 Final active atom (single-topology only).
--as, --activeStart=1 Starting active atom (single-topology only).
--ef1, --noElecFinal1=-1 Final no-electrostatics atom for 1st topology.
--ef2, --noElecFinal2=-1 Final no-electrostatics atom for 2nd topology
--es1, --noElecStart1=1 Starting no-electrostatics atom for 1st topology.
--es2, --noElecStart2=1 Starting no-electrostatics atom for 2nd topology
--f1, --final1=-1 Final ligand atom for the 1st topology.
--f2, --final2=-1 Final ligand atom for the 2nd topology
--la, --lastAtomID=-1 The last atom to test (default is to test all Atoms, unless a first atom is specified).
--la1, --ligAtoms1=-1 Period-separated ranges of 1st topology ligand atoms (e.g. 40-50.72-83).
--la2, --ligAtoms2=-1 Period-separated ranges of 2nd toplogy ligand atoms (e.g. 40-50.72-83)
--lm, --lambdaMoveSize=0.01 Size of the lambda moves during the test.
--ls, --lambdaScan Scan lambda values.
--np, --nParallel=1 Number of topologies to evaluate in parallel
--s1, --start1=0 Starting ligand atom for 1st topology.
--s2, --start2=0 Starting ligand atom for 2nd topology
--sdX, --skipdX Skip calculating per-atom dUdX values and only test lambda gradients.
--sf, --switchingFunction=1.0 Switching function to use for dual topology: options are TRIG, MULT, or a number (original behavior with specified lambda exponent)
--sk2, --skip2 Skip 2nd derivatives.
--tol, --tolerance=1.0e-3 The analytic vs. finite-difference gradient error tolerance.
--uaA, --unsharedA=-1 Unshared atoms in the A dual topology (period-separated hyphenated ranges)
--uaB, --unsharedB=-1 Unshared atoms in the B dual topology (period-separated hyphenated ranges)
-a, --atomID=1 The first atom to test (default is Atom 1)
-d, --dx=1.0e-5 The finite-difference step size.
-h, --help Print this help message.
-l, --lambda=-1 Initial lambda value.
-v, --verbose Print out the energy for each step.