Hi all,
I was trying to use the GAFF force field in LAMMPS, and I used the amber2lammp.py tool to convert the Amber data file to a LAMMPS data file.
One thing I noticed about the dihedral parameters is that in GAFF, the dihedral interaction is defined with a “1/2” factor in the constant term (see
http://ambermd.org/antechamber/gaff.html#function), and in the meantime, the dihedral (harmonic style) in LAMMPS doesn’t have the “1/2”. So intuitively, for one same dihedral, the value showing in a Amber data file should be 2 times larger than that in a LAMMPS data file. However, the LAMMPS data file generated by the amb2lmp tool gives the same value as in the Amber .top file.
Is it correct? I also checked the parameter values in the “gaff.lt” file in moltemplate (but didn’t use it), it should also yield the same value as the amb2lmp tool.
I tend to trust the converting by these tools, but just want to make sure…
Thanks in advance for any comments.
Btw, is there some way to compute the energy of one specific dihedral in LAMMPS. I noticed the “compute pe/atom” command, but one atom is always involved in more than one dihedrals. How to deal with that?
Thanks all,
Wei Ding
PhD student
Queen Mary University of London
London, UK