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?? 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? Thanks, Jesmin On Wed, Feb 27, 2013 at 10:33 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/27/13 10:25 AM, jesmin jahan wrote: >> >> Thanks Justin. >> Well, I am felling stupid now! Could you kindly provide me some better >> .mdp parameters that make more sense? >> >> gromacs 4.6 gives me error with my previous parameters which were >> working perfect in gromacs 4.5.3 >> >> It says we have to use cut-off verlet, either we have to use coupling >> temp or we have to set verlet-buffer-drift = -1. >> Then it says set pbc to xyz or xy. I tried to change my rlist or other >> cutoff values. It says box is too large or small. >> >> So, i am really very confused! >> It will be very kind of you, if you can suggest me some parameters >> which match best with my previous parameters namely: >> >> >>>> constraints = none >>>> integrator = md >>>> pbc = no >>>> dt = 0.001 >>>> nsteps = 0 >>>> rcoulomb = 300 >>>> rvdw = 300 >>>> rlist = 300 >>>> nstgbradii = 300 >>>> rgbradii = 300 >>>> implicit_solvent = GBSA >>>> gb_algorithm = HCT ; >>>> sa_algorithm = None >>>> gb_dielectric_offset = 0.02 >>>> >>>> optimize_fft = yes >>>> energygrps = protein >> >> ----------------------------- >> > > For implicit runs, I always set: > > pbc = no > ns_type = simple > comm-mode = angular > rlist = 0 > rcoulomb = 0 > rvdw = 0 > nstlist = 0 > rgbradii = 0 > nstgbradii = 1 > coulombtype = cutoff > vdwtype = cutoff > > > -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
