On Wed, 2012-02-29 at 11:12 -0700, Denny Frost wrote: > The parameters I used are from the following reference: > > Canongia Lopes and Padua, J. Phys. Chem. B 2004, 108, 16893 > > > This paper gives the bonded parameters of the anion and the non-bonded > parameters of both ions. The bonded parameters of the cation were > obtained (as indicated in the reference above) from the OPLS force > field. (Rizzo and Jorgensen, JACS 1999, 121, 4827).
> Fixing the dihedral error I mentioned in my last email has kept the > system from crashing. The coul. recip term is still positive, > however. > > > g_pme_error gave a Direct space error estimate of 9.8e-3 kJ/mol*nm and > a Reciprocal space error estimate of 3.3 kJ/mol*nm. > Look there is a big discrepancy between the real and reciprocal space error, such that your overall force has an error in the order of 10^0, but if you distribute the error over the real and reciprocal part by a change of ewald_rtol, you can descrease this error. g_pme_error with the flag -tune does this for you. Accordingly, by a decrease of the fourier spacing, the error can be further decreased to the desired accuracy. Hence you can check if the positive Coulomb term is an artefact of low accuracy. /Flo > On Wed, Feb 29, 2012 at 3:47 AM, Dommert Florian > <domm...@icp.uni-stuttgart.de> wrote: > 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 > > <domm...@icp.uni-stuttgart.de> 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 > > > <domm...@icp.uni-stuttgart.de> 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 > gmx-users@gromacs.org > > > > > > 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 > > gmx-users-requ...@gromacs.org. > > > > 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: domm...@icp.uni-stuttgart.de > > > Homepage: > > http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert > > > > > > Tel.: +49 - (0)711 - 68563613 > > > Fax.: +49 - (0)711 - 68563658 > > > > > > -- > > > gmx-users mailing list > gmx-users@gromacs.org > > > > 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 > > gmx-users-requ...@gromacs.org. > > > Can't post? Read > > http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > -- > > > gmx-users mailing list gmx-users@gromacs.org > > > > 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 > gmx-users-requ...@gromacs.org. > > > 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: domm...@icp.uni-stuttgart.de > > Homepage: > http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert > > > > Tel.: +49 - (0)711 - 68563613 > > Fax.: +49 - (0)711 - 68563658 > > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > 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 > gmx-users-requ...@gromacs.org. > > Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > 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 gmx-users-requ...@gromacs.org. > > 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: domm...@icp.uni-stuttgart.de > Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert > > Tel.: +49 - (0)711 - 68563613 > Fax.: +49 - (0)711 - 68563658 > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > 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: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658
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