Synopsis

test.MultiTopTimer [-ghvV] [--ac=<selection>] [--ac2=<selection>] [--acRes=<selection>] [--acRes2=<selection>] [-l=-1] [-n=5] [--np=1] [--nt=0] [--sf=1.0] [--uaA=-1] [--uaB=-1] [--uc=<selection>] [--uc2=<selection>] files…​

Description

Time energy and gradients for 1-4 topologies with optional lambda scaling.

Options

-h, --help

Print command help and exit.

-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].

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].

Timing Options

-g, --noGradient

Ignore computation of the atomic coordinates gradient.

-n, --iterations=5

Number of iterations.

--nt, --threads=0

Number of SMP threads (0 specifies use of all CPU cores).

-v, --verbose

Print the energy for each iteration.

Arguments

files…​

The atomic coordinate file in PDB or XYZ format.