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Merge pull request #1660 from tanmoy7989/reorder_remd_traj

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python tool to reorder replica traj
This commit is contained in:
Axel Kohlmeyer
2019-09-17 17:29:50 -04:00
committed by GitHub
parent fb7a439cd2 28b634f20d
commit 572235e66a
12 changed files with 1034 additions and 2 deletions
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19
doc/src/Tools.txt
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@ -76,9 +76,10 @@ Post-processing tools :h3
"pymol_asphere"_#pymol,
"python"_#pythontools,
"reax"_#reax_tool,
"replica"_#replica,
"smd"_#smd,
"spin"_#spin,
"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
"xmgrace"_#xmgrace :tb(c=6,ea=c,a=l)
Miscellaneous tools :h3
@ -485,6 +486,21 @@ README for more info on Pizza.py and how to use these scripts.
:line
replica tool :h4,link(replica)
The tools/replica directory contains the reorder_remd_traj python script which
can be used to reorder the replica trajectories (resulting from the use of the
temper command) according to temperature. This will produce discontinuous
trajectories with all frames at the same temperature in each trajectory.
Additional options can be used to calculate the canonical configurational
log-weight for each frame at each temperature using the pymbar package. See
the README.md file for further details. Try out the peptide example provided.
This tool was written by (and is maintained by) Tanmoy Sanyal,
while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)
:line
reax tool :h4,link(reax_tool)
The reax sub-directory contains stand-alone codes that can
@ -549,3 +565,4 @@ simulation.
See the README file for details.
These files were provided by Vikas Varshney (vv0210 at gmail.com)

8
doc/src/temper.txt
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@ -110,7 +110,13 @@ the information from the log.lammps file. E.g. you could produce one
dump file with snapshots at 300K (from all replicas), another with
snapshots at 310K, etc. Note that these new dump files will not
contain "continuous trajectories" for individual atoms, because two
successive snapshots (in time) may be from different replicas.
successive snapshots (in time) may be from different replicas. The
reorder_remd_traj python script can do the reordering for you
(and additionally also calculated configurational log-weights of
trajectory snapshots in the canonical ensemble). The script can be found
in the tools/replica directory while instructions on how to use it is
available in doc/Tools (in brief) and as a README file in tools/replica
(in detail).
The last argument {index} in the temper command is optional and is
used when restarting a tempering run from a set of restart files (one