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. 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 >
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