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import updated README file for charmm2lammps.pl with CMAP support

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Axel Kohlmeyer
2016-10-05 18:11:52 -04:00
parent 030df745bc
commit c07a01c661
1 changed files with 12 additions and 11 deletions
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23
tools/ch2lmp/README
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@ -24,11 +24,11 @@ To use the charmm2lammps.pl script, type: "perl charmm2lammps.pl
<forcefield> <project> [-option=value ...]" where <forcefield> is the
name of the CHARMM FF you are using, (i.e. all22_prot), and <project>
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"