Thank you, Mark. I think that running it on CPUs is a safer choice at present.
On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > Hi, > > It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the > original paper's coulomb settings can be taken with a grain of salt for use > with PME - others' success in practice should be a guideline here. The good > news is that the default GROMACS PME settings are pretty good for at least > some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the GPU > auto-tuning of parameters in 4.6 is designed to preserve the right sorts of > things. > > LJ is harder because it would make good sense to preserve the way CHARMM > did it, but IIRC you can't use something equivalent to the CHARMM LJ shift > with the Verlet kernels, either natively or with a table. We hope to fix > that in 5.0, but code is not written yet. I would probably use vdwtype = > cut-off, vdw-modifier = potential-shift-verlet and rcoulomb=rlist=rvdw=1.2, > but I don't run CHARMM simulations for a living ;-) > > Mark > > > On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan <rajatdesi...@gmail.com > >wrote: > > > Dear All, > > > > Any suggestions? > > > > Thank you. > > > > -- > > View this message in context: > > > http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > > -- > > 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 > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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
