Apr 6, 2011

How to generate LAMMPS data file with force field parameters

To make LAMMPS data file using pdb file in VMD,

1. load pdb file (or any molecule configuration file) in VMD

2. in VMD command line, type
topo writelammpsdata filename type
# type : full, atomic, etc..

3. a data file with filename is created in VMD folder

The "topotools" is a plugin for VMD.  https://sites.google.com/site/akohlmey/software/topotools

To make LAMMPS data file with force field parameters, "msi2lmp", a LAMMPS tool (/tools/msi2lmp/) can be used.

1. build msi2lmp
make   in /tools/msi2lmp/src/

2. msi2lmp.exe, force field file (e.g., cvff.frc), car and mdf files should be in same directory.
msi2lmp.exe rootname -class I -frc force_field_name
# rootname.cat
# rootname.mdf
# -class I (e.g, cvff), -class II (e.g., CFFx)
# -frc cvff   (cvff.frc)

3. rootname.lammps05 will be generated.

1 comment:

  1. But what if i want to modify these frc files? what do i do? Especially what do i do with the atom eqivalents?