On Mon, 2012-02-27 at 11:05 -0700, Denny Frost wrote: > The ionic liquid is bistriflate N-methyl-N-propyl pyrrolidinium and > the force field is from Lopes (CLaP). I tried deleting all of the > cation dihedrals from the itp file and found that the run did not > crash, although it still had a positive coul recip term. Upon > examination of the cation dihedrals I noticed that there was a typo in > which a set of unbonded carbons were put together in a dihedral term. > Perhaps this is what made the previous runs crash. > Even with this correction, the coul. recip. term is still positive. I > have tried smaller time steps and changing ewald_tol to 1e-3, but > these have not resolved this issue. How can I calculate the error in > the electrostatic force? > Denny >
The error of PME can be estimated a priori with the tool g_pme_error. I would suggest to tune it to a bound below 1e-3. I took a look at the force field parameters for the pyrrolidinium, which is published by Lopes in 2006, and I assume you use this parameters, are you ? I do not understand Table I in this paper. The dihedral parameters are just given for V_2 and V_4, and for a certain dihedral they are even set to zero. If you use this force field, how are the other parameters obtained ? Are they zero or do they correspond to the OPLS values given in the reference cited on the top of the table ? /Flo > On Sat, Feb 25, 2012 at 4:43 AM, Dommert Florian > <[email protected]> wrote: > 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 > > > -- > 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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