Force Field XBAR(1)
Synopsis
BAR [-hV] [--dV] [--eb] [--sa] [--ac=<selection>] [--ac2=<selection>] [--acRes=<selection>] [--acRes2=<selection>] [-e=1.0E-4] [--es=0] [-l=-1] [--l2=1.0] [--ni=1000] [--np=1] [--ns=2] [--sf=1.0] [--ss=0] [-t=298.15] [--uaA=-1] [--uaB=-1] [--uc=<selection>] [--uc2=<selection>] [files…]
Description
Evaluates a free energy change with the Bennett Acceptance Ratio algorithm using pregenerated snapshots.
Options
- --dV, --volume
- Write out snapshot volumes to the Tinker BAR file.
- -e, --eps=1.0E-4
- Specify convergence cutoff for BAR calculation.
- --eb, --evaluateBAR
- Evaluate Free Energy Differences from Tinker BAR files.
- --es, --endSnapshot=0
- End at this snapshot when reading in Tinker BAR files (indexed from 0).
- -h, --help
- Print command help and exit.
- --l2, --lambdaTwo=1.0
- Lambda value for the upper edge of the window
- --ni, --nIterations=1000
- Specify the maximum number of iterations for BAR convergence.
- --ns, --nStates=2
- If not equal to two, auto-determine lambda values and subdirectories (overrides other flags).
- --sa, --sortedArc
- If set, use sorted archive values.
- --ss, --startSnapshot=0
- Start at this snapshot when reading in Tinker BAR files (indexed from 0).
- -t, --temperature=298.15
- Temperature for system
- -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].