Thanks again Justin, I added
cutoff-scheme = group But still I am getting OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet which really says, openmp threads are supported only in Verlet! constraints = none integrator = md cutoff-scheme = group pbc = no ;verlet-buffer-drift = -1 dt = 0.001 nsteps = 0 ns_type = simple comm-mode = angular rlist = 0 rcoulomb = 0 rvdw = 0 nstlist = 0 rgbradii = 0 nstgbradii = 1 coulombtype = cutoff vdwtype = cutoff implicit_solvent = GBSA gb_algorithm = HCT ; sa_algorithm = None gb_dielectric_offset = 0.02 optimize_fft = yes energygrps = protein Best Regards, Jesmin On Wed, Feb 27, 2013 at 10:57 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/27/13 10:54 AM, jesmin jahan wrote: >> >> Many thanks to you Justin for your help. >> >> Now my .mdp file looks like: >> >> constraints = none >> integrator = md >> >> pbc = no >> verlet-buffer-drift = -1 >> dt = 0.001 >> nsteps = 0 >> ns_type = simple >> comm-mode = angular >> rlist = 0 >> rcoulomb = 0 >> rvdw = 0 >> nstlist = 0 >> rgbradii = 0 >> nstgbradii = 1 >> coulombtype = cutoff >> vdwtype = cutoff >> implicit_solvent = GBSA >> gb_algorithm = HCT ; >> sa_algorithm = None >> gb_dielectric_offset = 0.02 >> >> optimize_fft = yes >> energygrps = protein >> >> And when I run mdrun, it says >> >> "OpenMP threads have been requested with cut-off scheme Group, but >> these are only supported with cut-off scheme Verlet" >> >> Now if I add >> >> cutoff-scheme = Verlet >> >> It says >> >> With Verlet lists only full pbc or pbc=xy with walls is supported >> >> With Verlet lists nstlist should be larger than 0 >> >> >> So, what is the solution?? >> > > Use the group cutoff scheme rather than Verlet, otherwise we wind up right > back where we were before. > > >> Also, you told me >> >> "Note that implicit solvent calculations can be run on no more than 2 >> processors. You'll get a fatal error if you try to use more." >> >> Is there any documentation for this? Can I cite you if I want to add >> this information in an article? >> > > It's a bug, listed on Redmine somewhere. I doubt that requires any sort of > citation, but if anyone asks, there are discussions in the list archive and > on redmine.gromacs.org. > > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 -- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790. -- 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
