Merge pull request #791 from akohlmey/charmm-cmap-docs-reference (10d80ba9) · Commits · 郑智淋 / lammps

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)

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		@@ -120,6 +120,10 @@ quantity being minimized), you MUST enable the

		[Restrictions:]

		To function as expected this fix command must be issued {before} a
		"read_data"_read_data.html command but {after} a
		"read_restart"_read_restart.html command.

		This fix can only be used if LAMMPS was built with the MOLECULE
		package. See the "Making
		LAMMPS"_Section_start.html#start_3 section for more info on packages.

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		# Created by charmm2lammps v1.9.1 on Wed Oct 5 18:08:55 EDT 2016
		# Command: charmm2lammps.pl -water -ions -border=2.0 all36_prot 1gb1
		# Created by charmm2lammps v1.9.1 on Sun Jan 28 05:50:21 EST 2018
		# Command: charmm2lammps.pl -border=2.0 -cmap=36 -ions -water all36_prot 1gb1

		units real
		neigh_modify delay 2 every 1
		@@ -14,7 +14,10 @@ pair_style lj/charmm/coul/long 8 12
		pair_modify mix arithmetic
		kspace_style pppm 1e-6

		read_data 1gb1.data
		# Modify following line to point to the desired CMAP file
		fix cmap all cmap charmm36.cmap
		fix_modify cmap energy yes
		read_data 1gb1.data fix cmap crossterm CMAP

		special_bonds charmm
		thermo 10