Hi, I imagine nobody has ever tried with Verlet plus freeze plus annealing, so it could be broken somehow... But frozen atoms around a cavity and no electric field from solvent sounds like a model highly unlikely to be related to reality...
Mark On Fri, 4 Aug 2017 18:55 <nikol...@spbau.ru> wrote: > Hello! > > I want to run dynamics only for a relatively small cavity of my molecule, > with all other atoms frozen. For this reason, I also don't use solvent, > because it won't move anyway. I run the simulation on GPU (gromacs 5.1.2), > i.e. I use the Verlet scheme, pbc = xyz. However, when I start running > simulations, I get violent behavior: the molecule immediately falls > apart!! I am sure that I just made a silly thing in the parameters, but > what is it? Here I attach my dynamics .mdp parameters: > > > define = -DPOSRES > integrator = md > dt = 0.001 > nsteps = 1200000 > > nstxout = 1000 > nstvout = 1000 > nstxtcout = 1000 > nstlog = 100 > nstenergy = 1000 > > continuation = no > constraints = none > > tcoupl = V-rescale > tc_grps = System > tau_t = 0.1 > ref_t = 0 > > cutoff-scheme = Verlet > ns_type = grid > nstlist = 10 > rcoulomb = 0.9 > rvdw = 0.9 > > coulombtype = PME > pme_order = 4 > fourierspacing = 0.16 > > pbc = xyz > gen_vel = no > > DispCorr = EnerPres > > ; > ; Freezing atoms # this is all the atoms except for the cavity inside > ; > freezegrps = GroupDyna > freezedim = Y Y Y > ; > ; Heating > ; > annealing = single > annealing_npoints = 2 > annealing_time = 0 50 > annealing_temp = 0 298 > > > Thank you in advance, > Dmitrii. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.