test.MultiTopTimer(1) Manual Page

Name

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

Synopsis

test.MultiTopTimer [-gghvvV] [--ac=<selection>] [--ac=<selection>] [--ac2=<selection>] [--ac2=<selection>] [-l=-1] [-l=-1] [-n=5] [-n=5] [--np=1] [--np=1] [--nt=0] [--nt=0] [--sf=1.0] [--sf=1.0] [--uaA=-1] [--uaA=-1] [--uaB=-1] [--uaB=-1] [--uc=<selection>] [--uc=<selection>] [--uc2=<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].
-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].
--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.