Thank you for the response.
On Fri, Apr 10, 2020 at 9:02 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/10/20 8:13 AM, Alex wrote: > > Dear Justin, > > Any comment please? > > Sorry, haven't had power/network for a while due to some bad storms here. > > GROMOS force fields are parametrized assuming all bonds are fixed, so > your constraints should be "all-bonds" not "h-bonds." > Interesting, hopefully that is the problem. > > I would also suggest you thoroughly validate the quality of the epoxy > molecule topology against QM data and bulk-phase properties, if possible. > As the ATB folks claim, the parameterization has been performed against a very high level DFT calculation, especially for the molecules with less than 50 atoms. I already have tested the density and it is in agreement with the experimental value. Regarding the "comm-grps = " , would you also please kindly let me know which one you would recommend for this system + plus a small single molecule called MOL_A which defuses from water inside the epoxy, specially for the PMF calculation of the Mol_A? comm-grps = Other SOL ;; (Other = thin_film and Mol_A) or comm-grps = system Thank you Alex > > -Justin > > > 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. > >>> > > -- > ================================================== > > 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.