test.SortXPH(1) Manual Page

Name

test.SortXPH - The SortXPH command unwinds .ARC files from CpHMD runs.

Synopsis

test.SortXPH [-hV] [--bT] [--ac2=<selection>] [--ac2=<selection>] [--ex=0.5] [--np=1] [--np=1] [--nw=-1] [--pH=7.4] [--pHGaps=1] [--sf=1.0] [--sf=1.0] [--sT=298.15] [--uaA=-1] [--uaA=-1] [--uaB=-1] [--uaB=-1] [--uc2=<selection>] [--uc2=<selection>] file

Description

The SortXPH command unwinds .ARC files from CpHMD runs.

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).
--pH=7.4: Sets the middle of the pH ladder
--pHGaps=1: Sets the size of the gaps in the pH ladder
--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 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

file: Trajectory files for the first end of the window, followed by trajectories for the other end