OK, that is what I was trying to figure out -- is the problem reproducible on both GPU and CPU. Now, you havent answered the direct question, if the energies are the same for at least the first 5 steps are so -- without that knowledge, then here might be different errors occurring in GPU vs CPU.
At this point, the question is then whether this works with another code with the same input parameters. Sander (part of the AmberTools system)is downloadable (I believe to anyone, not just academics), so you can try running the same system on Sander, using the best fit to the implicit solvent model in gromacs. If THAT works, and Gromacs GPU fails, then it would appear to be a problem with Gromacs implicit solvent implementation, and should be posted to redmine as a bug, as well as described on the list with full details (more than you have provided so far!) so that it can be reproduced by the developers. Best, On Tue, Jan 25, 2011 at 5:05 AM, K. Singhal <k.sing...@uva.nl> wrote: > Hi > > It's not necessarily GPU-specific, it's implicit solvent-specific. I don't > get these problems in explicit solvent simulations on CPU, only in implicit > solvent simulations both on GPU as well as CPU. One of the problems that I > can think of is unbalanced charges that I would have balanced out using NaCl > ions, but not any more. > > Regards > Kush > > > > -- > Kushagra Singhal > Promovendus, Computational Chemistry > van 't Hoff Institute of Molecular Sciences > Science Park 904, room C2.119 > 1098 XH Amsterdam, The Netherlands > +31 205256965 > Universiteit van Amsterdam > k.sing...@uva.nl > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
