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.
