[gmx-users] How to list OPLS parameters

[Mark Abraham]

On 10/11/2011 12:52 AM, Thomas Schlesier wrote:
> Hi all,
> for a publication i want to list the used OPLS parameters for the 
> investigated molecules. In GROMACS all atomtypes are uniquely defined 
> by the atomtype `opls_xyz`. And from the atomtypes one can deduct the 
> bonded parameters. So it is sufficient to list only the atomtypes and 
> probably charges.
> My question is now, is this definition common knowledge, or only 
> GROMACS-intern? From the header of `ffoplsaa.atp` one sees that the 
> first 65 atomtypes are for the OPLS-UA force field, and the names of 
> the atomtypes are the same as in the paper which is mentioned.
> Concerning the OPLS-AA force field, is there the GROMACS numbering 
> scheme also common knowledge?

If you consult the paper in which OPLS-AA was published (which you no 
doubt read before simulating with OPLS-AA), you will see that the 
numbering scheme is not internal to GROMACS.

Mark