On Fri, 2012-02-24 at 11:03 -0700, Denny Frost wrote: > Thank you both for your replies. I currently have another ionic > liquid running just fine on the same gromacs build (compiled the tpr > file yesterday), so I am reluctant to conclude that the problem is > with the linking. Please let me know if you disagree. > The force field I am using was published in 2004 and has been > validated by another group. I have double and triple checked my itp > files to make sure they match the force field, but it's possible there > are still some errors there.
Is it the force field of Lopes (CLaP) et al. or Liu et al. (LHW) and who validated it, I am just curious, and what is the ionic liquid ? Though you are constraining the hbonds, I would be cautious with the time step of 2fs, because it might be, that the eigenfrequency of the anionic bonds requires a shorter time step, but this should not be the problem of a positive Coulomb energy. Have you calculated the error in the electrostatic force ? I would suggest to tune it to a limit of 1e-3, perhaps this resolves the problem of the positive Coulomb term. Perhaps some 1--4 and dihedral interactions are missing in the itp file, so assure if all of them are provided correctly. /Flo > I agree that this is very strange and feel that there must be > something fundamentally wrong in the mdp file or deeper. I have > included my mdp file below. > > > title = PMP+TFN > cpp = /lib/cpp > constraints = hbonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 10000000 ; total 20 ns > nstcomm = 10 > nstxout = 50000 > nstvout = 50000 > nstfout = 0 > nstlog = 5000 > nstenergy = 5000 > nstxtcout = 25000 > nstlist = 10 > ns_type = grid > pbc = xyz > coulombtype = PME > vdwtype = Cut-off > rlist = 1.2 > rcoulomb = 1.2 > rvdw = 1.2 > fourierspacing = 0.12 > pme_order = 4 > ewald_rtol = 1e-5 > ; Berendsen temperature coupling is on in two groups > Tcoupl = v-rescale > tc_grps = PMP TFN > tau_t = 0.2 0.2 > ref_t = 300 300 > nsttcouple = 1 > ; Energy monitoring > energygrps = PMP TFN > ; Isotropic pressure coupling is now on > Pcoupl = berendsen > pcoupltype = isotropic > tau_p = 2.0 > ref_p = 1.0 > compressibility = 4.5e-5 > > > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp = 300.0 > gen_seed = -1 > > > > On Fri, Feb 24, 2012 at 12:17 AM, Dommert Florian > <[email protected]> wrote: > On Thu, 2012-02-23 at 13:35 -0700, Denny Frost wrote: > > Dear all, > > I am trying to equilibrate a solvent of pure ionic liquid. > The system > > keeps exploding (after 2-5 ns) and I am not sure why, though > I believe > > coulombic interactions are to blame. This is because the > Coul-SR term > > is negative, but the Coul. recip term is very positive > throughout the > > entire run (giving the entire system a positive potential > energy). I > > think this means that the short-range electrostatics are > okay, but the > > long range electrostatics (calculated with PME) are not. > Does anybody > > have any suggestions as to why this would happen? I have > used the > > exact same PME input parameters for another ionic liquid > that works > > just fine. They are listed below. > > > > > > rcoulomb = 1.2 > > fourierspacing = 0.12 > > pme_order = 4 > > ewald_rtol = 1e-5 > > > > > Depends on the force field you are using. Perhaps it ist not > validated > for the ionic liquid you want to study. It is especially > strange, that > it takes so long for your system to blow up. > > Moreoever I would try to optimize the PME settings with the > tools, > g_tune_pme and g_pme_error, which give you performance and > accuracy of > the parameters, respectively. > > So perhaps with some more information I can provide more help. > > /Flo > > > > > Thanks! > > Denzil Frost > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > > Please don't post (un)subscribe requests to the list. Use > the > > www interface or send it to [email protected]. > > Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > -- > Florian Dommert > Dipl. - Phys. > > Institute for Computational Physics > University Stuttgart > > Pfaffenwaldring 27 > 70569 Stuttgart > > EMail: [email protected] > Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert > > Tel.: +49 - (0)711 - 68563613 > Fax.: +49 - (0)711 - 68563658 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: [email protected] Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658
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