Does anyone have a "reference manual" of such forcefield? (especially the related top files in GROMACS)
e.g. what are the atom types included and what they describe, etc. etc.
Check atomtypes.atp in oplsaa.ff - it has descriptions of every atom type, except the UA ones, which are pretty much never used.
If you have an especial problem I can help as I regularly work with OPLS-AA in GROMACS. Anyway, in GROMACS regardless of the name of atoms you have in your initial structure (either .PDB or .gro) you should assign an atom type to each atom which helps GROMACS to find appropriate parameter for each atom. In OPLS-AA These parameters has been assigned to atoms in many common chemicals (mostly organics). If you have GROMACS installed on your machine go to
"/gromacs/share/gromacs/top" and you will find the opls-aa folder. inside the folder there is a file named "atomtypes.ato". If you open the file you will see all atom types and their definition and references you need.
According to these atom types all bonds, angles and torsion potentials have been defined in ffbonded.itp and ffnonbonded.itp in the same folder. When you use pdb2gmx for your system to generate the .top file, gromacs use these parameters for your system.
If you need a ref for phillosophy of OPLS-AA force field and how (and with which data) it has been parametrized you can have look on this paper:
http://pubs.acs.org/doi/abs/10.1021/ja9621760
Regards
Hi Abolfazl,
I need to find the OPLS-AA parameters for a compound that I have. I use lammps. Could you please assist me in finding the parameters with OPLS-AA in Gromacs? I can send my pdb file for you if you have time.
Kind regards,
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