Allowed force fields in GPU-GROMACS?

vijay singh · Post by **vijay singh** » Mon Sep 14, 2009 11:29 pm

Hi,

I am using a 64 bit linux cuda system with the latest version of Gromacs.

Q1) Are all the force fields presented by pdb2gmx available to be incorporated on the gpu-gromacs?

0: GROMOS96 43a1 force field
1: GROMOS96 43a2 force field (improved alkane dihedrals)
2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
6: [DEPRECATED] Gromacs force field (see manual)
7: [DEPRECATED] Gromacs force field with hydrogens for NMR
8: Encad all-atom force field, using scaled-down vacuum charges
9: Encad all-atom force field, using full solvent charges

Q2) I seem to be having trouble with the energy file, in that the file (*.edr) remains empty. Any reasons why that could be happening?

Thanks,
VJ

Peter Eastman · Post by **Peter Eastman** » Tue Sep 15, 2009 1:45 pm

> Q1) Are all the force fields presented by pdb2gmx available to be incorporated on the gpu-gromacs?

No, some of them use functional forms that aren't supported by OpenMM. The only force field that is *fully* supported is AMBER, which you can get from

http://chemistry.csulb.edu/ffamber/

OPLS is *almost* fully supported. The only problem is that OpenMM uses Lorentz-Bertelot combining rules for Lennard-Jones interactions, not the Jorgensen combining rules that OPLS calls for. This will make a slight (but probably very small) difference in your results.

> Q2) I seem to be having trouble with the energy file, in that the file (*.edr) remains empty. Any reasons why that could be happening?

Make sure you're using PR4, since earlier releases didn't output energies. In PR4 the following energy terms should be reported correctly: potential energy, kinetic energy, total energy, and temperature. All other values in the edr file will be zero.

Peter

vijay singh · Post by **vijay singh** » Wed Sep 16, 2009 9:37 am

Thanks Peter,

We are working on the force field porting and hope to be completed with it shortly.

For the energy, I am using PR4, but may be I should double check my flag settings.

Thanks Again,
VJ

Allowed force fields in GPU-GROMACS?

Allowed force fields in GPU-GROMACS?

RE: Allowed force fields in GPU-GROMACS?

RE: Allowed force fields in GPU-GROMACS?