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