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test.SortXPH(1) Manual Page

Name

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

Synopsis

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

--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