Dear Justin, Any comment please? Regards, Alex
On Tue, Apr 7, 2020 at 5:38 PM Alex <alexanderwie...@gmail.com> wrote: > Thanks Justin for the response. > Please find below the mdp file. > The system is a thin film made out of a epoxy molecule, picture in be > below link, with water on top and bottom of the film. I even sometimes have > the same issue when I simulate the bulk of this system, I mean a cubic box > filled by this molecule and no water. > I got the force fields from the latest version of ATB repository by which > I have previously done some other simulation for the same molecule. > > https://drive.google.com/open?id=1tJLxh9jQ2v5DDTrVR8IuQz40B3NN0zlb > > %--------mdp------- > title = Thin-Film > integrator = md > dt = 0.002 ; 2 fs ;0.001 1 fs > nsteps = 25000000 ; 50 ns ;50000000 ; 50 ns > xtc-precision = 500 ; 1000 > ;nstlist = 40 > %----------------- > ;;in .trr file > nstxout = 3000 ; 6000 > nstvout = 0 > nstfout = 0 > ;;in energy file.log > nstlog = 2000 ; 4000 > nstcalcenergy = 2000 ;4000 > nstenergy = 2000 ;4000 > ;;in xtc file > nstxout-compressed = 0 > ;compressed-x-grps = non-Water > %----------------- > continuation = yes > gen-vel = no > constraint-algorithm = lincs > constraints = h-bonds > cutoff-scheme = Verlet > coulombtype = PME > rcoulomb = 1.4 > > vdwtype = Cut-off > rvdw = 1.4 > DispCorr = EnerPres > > tcoupl = v-rescale > tc-grps = system > tau-t = 1.5 > nhchainlength = 10 > ref-t = 298.15 > pbc = xyz > > pcoupl = Parrinello-Rahman > Pcoupltype = isotropic > tau_p = 2.5 > compressibility = 4.5e-5 > ref_p = 1.0 > refcoord-scaling = com > energygrps = thin_film SOL > comm-mode = Linear > nstcomm = 100 > comm-grps = Thin_fiml SOL > %------------------------- > > Thank you > Alex > > On Tue, Apr 7, 2020 at 5:06 PM Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 4/7/20 5:00 PM, Alex wrote: >> > Dear all, >> > After minimization and equalizations using nvt (v-rescale) and npt (both >> > berendsen and ;Parrinello-Rahman), a simulation of mine could run well >> for >> > 200 ns using dt =0.001 while it would crash after 3 ns If I used dt = >> 0.002 >> > with the particles communication fatal error. >> > >> > Fatal error: >> > 2 particles communicated to PME rank 12 are more than 2/3 times the >> cut-off >> > out of the domain decomposition cell of their charge group in dimension >> y. >> > This usually means that your system is not well equilibrated. >> > >> > So, if the system would not be well equlibrated, then I would expect >> that >> > with dt = 0.001 the simulation wouldn't run well for 200 ns. But I >> expect >> > that it also crashes for example around 6 ns as the with the dt = 0.002 >> the >> > simulation last only 3 ns. >> > >> > Any comment that helps to understand the problem would be highly >> > appreciated. >> >> Please provide a description of what your system is and a full .mdp >> file. While most of the time these crashes come from poor equilibration, >> an inadequately parametrized topology or bad combination/misuse of >> algorithms can also cause crashes. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Assistant Professor >> Office: 301 Fralin Hall >> Lab: 303 Engel Hall >> >> Virginia Tech Department of Biochemistry >> 340 West Campus Dr. >> Blacksburg, VA 24061 >> >> jalem...@vt.edu | (540) 231-3129 >> http://www.thelemkullab.com >> >> ================================================== >> >> -- >> 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.