Force Field XSortArc(1)
Synopsis
SortArc [-hV] [--bT] [--ac=<selection>] [--ac2=<selection>] [--acRes=<selection>] [--acRes2=<selection>] [--ex=0.5] [-l=-1] [--np=1] [--nw=-1] [--sf=1.0] [--sT=298.15] [--uaA=-1] [--uaB=-1] [--uc=<selection>] [--uc2=<selection>] files…
Options
- --bT, --sortByTemp
- If set, sort archive files by temperature values
- --ex, --exponent=0.5
- Sets the exponent for the exponential temperature ladder if sorting by temperature.
- -h, --help
- Print command help and exit.
- --nw, --nWindows=-1
- If set, auto-determine lambda values and subdirectories (overrides other flags).
- --sT, --startTemp=298.15
- Sets the starting temperature for the exponential temperature ladder if sorting by temperature.
- -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].