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clarify ch2lmp commands purpose in tools section

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Axel Kohlmeyer 2018-01-28 06:19:33 -05:00
parent 5e9d257ec2
commit ba68548e38
2 changed files with 9 additions and 14 deletions
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11
doc/src/Section_tools.txt
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@ -111,14 +111,21 @@ back-and-forth between the CHARMM MD code and LAMMPS.
They are intended to make it easy to use CHARMM as a builder and as a
post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a
PDB file with associated CHARMM info, including CHARMM force field
data, into its LAMMPS equivalent. Using lammps2pdb.pl you can convert
LAMMPS atom dumps into PDB files.
data, into its LAMMPS equivalent. Support for the CMAP correction of
CHARMM22 and later is available as an option. This tool can also add
solvent water molecules and Na+ or Cl- ions to the system.
Using lammps2pdb.pl you can convert LAMMPS atom dumps into PDB files.
See the README file in the ch2lmp sub-directory for more information.
These tools were created by Pieter in't Veld (pjintve at sandia.gov)
and Paul Crozier (pscrozi at sandia.gov) at Sandia.
CMAP support added and tested by Xiaohu Hu (hux2 at ornl.gov) and
Robert A. Latour (latourr at clemson.edu), David Hyde-Volpe, and
Tigran Abramyan, (Clemson University) and
Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
:line
chain tool :h4,link(chain)

12
tools/ch2lmp/main_manual
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@ -1,12 +0,0 @@
The charmm2lmp sub-directory contains tools for converting files back-and-forth between
the CHARMM MD code and LAMMPS.
The charmm2lammps.pl perl script converts CHARMM input files into LAMMPS input.
The lammps2pdb.pl perl script converts LAMMPS dump files into a pdb series file.
The mkpdb.f fortran 90 code also converts LAMMPS dump files into PDB files, and the
mkdcd.f tool converts LAMMPS dump files into CHARMM *.dcd trajectory files that can
be read-in to CHARMM for analysis. See the README file in the charmm2lmp sub-directory
for more information.
These tools were written by Pieter J. in 't Veld (pjintve@sandia.gov) and Paul Crozier
(pscrozi@sandia.gov) at Sandia.