Thank you all for the reply, now I'm much less confuse and thank you David for the paper.
I wanted to try implicit simulations because I need to speed up a bit my simulations...but I think that now I'll try something else (coarse grained/remd). cheers Fra On Mon, 23 Sep 2013, at 08:28 PM, David van der Spoel wrote: > On 2013-09-23 20:23, Justin Lemkul wrote: > > > > > > On 9/23/13 2:08 PM, Szilárd Páll wrote: > >> Hi, > >> > >> Admittedly, both the documentation on these features and the > >> communication on the known issues with these aspects of GROMACS has > >> been lacking. > >> > >> Here's a brief summary/explanation: > >> - GROMACS 4.5: implicit solvent simulations possible using mdrun-gpu > >> which is essentially mdrun + OpenMM, hence it has some limitations, > >> most notably it can only run on a single GPU. The performance, > >> depending on setting, can be up to 10x higher than on the CPU. > >> - GROMACS 4.6: the native GPU acceleration does supports only explicit > >> solvent, mdrun + OpenMM is still available (exactly for implicit > >> solvent runs), but has been moved to the "contrib" section which means > >> that it is not fully supported. Moreover, OpenMM support - unless > >> somebody volunteers for maintenance of the mdrun-OpenMM interface - > >> will be dropped in the next release. > >> > >> I can't comment much on the implicit solvent code on the CPU side > >> other than the fact that there have been issues which AFAIK limit the > >> parallelization to a rather small number of cores, hence the > >> achievable performance is also limited. I hope others can clarify this > >> aspect. > >> > > > > I never got the implicit code to run on more than 2 CPUs, and as I > > recall Berk hard-coded this due to a limitation involving constraints. > > It's been a couple years since I tried anything with implicit since (1) > > the OpenMM support was so buggy and incomplete on GPU and (2) the code > > ran an order of magnitude slower on CPU than the explicit solvent > > counterpart. > > > > -Justin > > > And finally, even though this is not what you were asking, and likely > not wanted to hear either: with implicit solvent your results will not > be general enough to be useful, if e.g. hydrogen bonds are important. I > would like to recommend my latest paper which shows how solvent entropy > and enthalpy contribute in a complex manner to non-bonded interactions > in a way that implicit solvent never could: > > http://pubs.acs.org/doi/abs/10.1021/ct400404q > > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > 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 -- Francesco Carbone PhD student Institute of Structural and Molecular Biology UCL, London fra.carbone...@ucl.ac.uk -- 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