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.