From c07a01c661d6532bdfe54404f6d7aadb2daa6926 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 5 Oct 2016 18:11:52 -0400 Subject: [PATCH] import updated README file for charmm2lammps.pl with CMAP support --- tools/ch2lmp/README | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/tools/ch2lmp/README b/tools/ch2lmp/README index 25c0a7a9a0..4b950b59d4 100644 --- a/tools/ch2lmp/README +++ b/tools/ch2lmp/README @@ -24,11 +24,11 @@ To use the charmm2lammps.pl script, type: "perl charmm2lammps.pl [-option=value ...]" where is the name of the CHARMM FF you are using, (i.e. all22_prot), and is the common name of your *.crd and *.psf files. Possible options -are listed next. If the option requires a parameter, the syntax -should be -option=value (e.g. -border=5). +are listed below. If the option requires a parameter, the syntax +must be like this: -option=value (e.g. -border=5). -help display available options --charmm add charmm types to LAMMPS data file +-nohints do not add charmm types and style hints to LAMMPS data file -water add TIP3P water [default: 1 g/cc] -ions add (counter)ions using Na+ and Cl- [default: 0 mol/l] -center recenter atoms @@ -42,9 +42,8 @@ should be -option=value (e.g. -border=5). -ax rotation around x-axis -ay rotation around y-axis -az rotation around z-axis --cd correction for dihedral for carbohydrate systems -cmap add CMAP section to data file and fix cmap command lines in - input script" (NOTE: requires use of *.pdb file) + input script" (NOTE: requires use of *.pdb file) In the "example" folder, you will find example files that were created by following the steps below. These steps describe how to take a @@ -89,9 +88,9 @@ exit 1ac7.pdb file. 6) Run charmm2lammps.pl by typing: -"perl charmm2lammps.pl all27_na 1ac7 -charmm -border=1 -pdb_ctrl -water -ions" +"perl charmm2lammps.pl all27_na 1ac7 -border=1 -pdb_ctrl -water -ions" -7) Run lammps by typing: "lmp < 1ac7.in" +7) Run lammps by typing: "lmp_mpi -in 1ac7.in" 8) Run lammps2pdb.pl by typing: "perl lammps2pdb.pl 1ac7" @@ -102,10 +101,11 @@ molecule and converts them into LAMMPS format. The -water option embeds the molecule in water on a crystal lattice. The -border option includes a layer of water surrounding the minimum dimensions of the molecule. The -pdb_ctrl option produces the 1ac7_ctrl.pdb file that -can be visualized in a standard visualization package such as VMD. The --charmm option put comments into the LAMMPS data file (everything +can be visualized in a standard visualization package such as VMD. By +default, comments are added into the LAMMPS data file (everything after the # sign is a comment) for user convenience in tracking atom -types etc. according to CHARMM nomenclature. +types etc. according to CHARMM nomenclature. If this is not desired, +the -nohints option can be used to turn off this function. The example molecule provided above (i.e., 1ac7) is a DNA fragment. If instead, a peptide longer than 2 amino acid residues or a protein @@ -131,7 +131,7 @@ speed. The -ions option allows the user to neutralize the simulation cell with Na+ or Cl- counterions if the molecule has a net charge Additional salt can be added by increasing the default concentration -(e.g. -ions=0.5). +(i.e., -ions=0.5). ** In the "other" file folder, you will find: @@ -146,3 +146,4 @@ Additional salt can be added by increasing the default concentration 3) A 3rd party perl script called "crd2pdb.pl" 4) A 3rd party fortran code called "pdb_to_crd.f" +