Well, that means that I need to use the group scheme? Or I can just add solvent and run the same thing?
> 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. > -- 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.
