BAR(1) Manual Page

Name

BAR - Evaluates a free energy change with the Bennett Acceptance Ratio algorithm using pregenerated snapshots.

Synopsis

BAR [-hV] [--dV] [--sa] [--tb] [--utb] [--ac=<selection>] [--ac2=<selection>] [--es=0] [-l=-1] [--l2=1.0] [--np=1] [--nw=-1] [--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.
--es, --endSnapshot=0: End at this snapshot when reading in tinker BAR files.
-h, --help: Print command help and exit.
--l2, --lambdaTwo=1.0: Lambda value for the upper edge of the window
--nw, --nWindows=-1: If set, 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.
-t, --temperature=298.15: Temperature for system
--tb, --tinkerBAR: Write out a Tinker BAR file.
--utb, --useTinker: If set, use tinker BAR files for energy snapshots.
-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].

Arguments

files…: A single PDB/XYZ when windows are auto-determined (or two for dual topology). Two trajectory files for BAR between two ensembles (or four for dual topology).