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. <div>
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?</div>
<div>Denny<br><br><div class="gmail_quote">On Sat, Feb 25, 2012 at 4:43 AM, Dommert Florian <span dir="ltr"><<a href="mailto:dommert@icp.uni-stuttgart.de">dommert@icp.uni-stuttgart.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On Fri, 2012-02-24 at 11:03 -0700, Denny Frost wrote:<br>
> Thank you both for your replies. I currently have another ionic<br>
> liquid running just fine on the same gromacs build (compiled the tpr<br>
> file yesterday), so I am reluctant to conclude that the problem is<br>
> with the linking. Please let me know if you disagree.<br>
> The force field I am using was published in 2004 and has been<br>
> validated by another group. I have double and triple checked my itp<br>
> files to make sure they match the force field, but it's possible there<br>
> are still some errors there.<br>
<br>
</div>Is it the force field of Lopes (CLaP) et al. or Liu et al. (LHW) and who<br>
validated it, I am just curious, and what is the ionic liquid ?<br>
<br>
Though you are constraining the hbonds, I would be cautious with the<br>
time step of 2fs, because it might be, that the eigenfrequency of the<br>
anionic bonds requires a shorter time step, but this should not be the<br>
problem of a positive Coulomb energy. Have you calculated the error in<br>
the electrostatic force ? I would suggest to tune it to a limit of 1e-3,<br>
perhaps this resolves the problem of the positive Coulomb term.<br>
<br>
Perhaps some 1--4 and dihedral interactions are missing in the itp file,<br>
so assure if all of them are provided correctly.<br>
<br>
/Flo<br>
<div class="HOEnZb"><div class="h5"><br>
> I agree that this is very strange and feel that there must be<br>
> something fundamentally wrong in the mdp file or deeper. I have<br>
> included my mdp file below.<br>
><br>
><br>
> title = PMP+TFN<br>
> cpp = /lib/cpp<br>
> constraints = hbonds<br>
> integrator = md<br>
> dt = 0.002 ; ps !<br>
> nsteps = 10000000 ; total 20 ns<br>
> nstcomm = 10<br>
> nstxout = 50000<br>
> nstvout = 50000<br>
> nstfout = 0<br>
> nstlog = 5000<br>
> nstenergy = 5000<br>
> nstxtcout = 25000<br>
> nstlist = 10<br>
> ns_type = grid<br>
> pbc = xyz<br>
> coulombtype = PME<br>
> vdwtype = Cut-off<br>
> rlist = 1.2<br>
> rcoulomb = 1.2<br>
> rvdw = 1.2<br>
> fourierspacing = 0.12<br>
> pme_order = 4<br>
> ewald_rtol = 1e-5<br>
> ; Berendsen temperature coupling is on in two groups<br>
> Tcoupl = v-rescale<br>
> tc_grps = PMP TFN<br>
> tau_t = 0.2 0.2<br>
> ref_t = 300 300<br>
> nsttcouple = 1<br>
> ; Energy monitoring<br>
> energygrps = PMP TFN<br>
> ; Isotropic pressure coupling is now on<br>
> Pcoupl = berendsen<br>
> pcoupltype = isotropic<br>
> tau_p = 2.0<br>
> ref_p = 1.0<br>
> compressibility = 4.5e-5<br>
><br>
><br>
> ; Generate velocites is on at 300 K.<br>
> gen_vel = yes<br>
> gen_temp = 300.0<br>
> gen_seed = -1<br>
><br>
><br>
><br>
> On Fri, Feb 24, 2012 at 12:17 AM, Dommert Florian<br>
> <<a href="mailto:dommert@icp.uni-stuttgart.de">dommert@icp.uni-stuttgart.de</a>> wrote:<br>
> On Thu, 2012-02-23 at 13:35 -0700, Denny Frost wrote:<br>
> > Dear all,<br>
> > I am trying to equilibrate a solvent of pure ionic liquid.<br>
> The system<br>
> > keeps exploding (after 2-5 ns) and I am not sure why, though<br>
> I believe<br>
> > coulombic interactions are to blame. This is because the<br>
> Coul-SR term<br>
> > is negative, but the Coul. recip term is very positive<br>
> throughout the<br>
> > entire run (giving the entire system a positive potential<br>
> energy). I<br>
> > think this means that the short-range electrostatics are<br>
> okay, but the<br>
> > long range electrostatics (calculated with PME) are not.<br>
> Does anybody<br>
> > have any suggestions as to why this would happen? I have<br>
> used the<br>
> > exact same PME input parameters for another ionic liquid<br>
> that works<br>
> > just fine. They are listed below.<br>
> ><br>
> ><br>
> > rcoulomb = 1.2<br>
> > fourierspacing = 0.12<br>
> > pme_order = 4<br>
> > ewald_rtol = 1e-5<br>
> ><br>
><br>
><br>
> Depends on the force field you are using. Perhaps it ist not<br>
> validated<br>
> for the ionic liquid you want to study. It is especially<br>
> strange, that<br>
> it takes so long for your system to blow up.<br>
><br>
> Moreoever I would try to optimize the PME settings with the<br>
> tools,<br>
> g_tune_pme and g_pme_error, which give you performance and<br>
> accuracy of<br>
> the parameters, respectively.<br>
><br>
> So perhaps with some more information I can provide more help.<br>
><br>
> /Flo<br>
><br>
> ><br>
> > Thanks!<br>
> > Denzil Frost<br>
> > --<br>
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><br>
> --<br>
> Florian Dommert<br>
> Dipl. - Phys.<br>
><br>
> Institute for Computational Physics<br>
> University Stuttgart<br>
><br>
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> 70569 Stuttgart<br>
><br>
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<br>
--<br>
Florian Dommert<br>
Dipl. - Phys.<br>
<br>
Institute for Computational Physics<br>
University Stuttgart<br>
<br>
Pfaffenwaldring 27<br>
70569 Stuttgart<br>
<br>
EMail: <a href="mailto:dommert@icp.uni-stuttgart.de">dommert@icp.uni-stuttgart.de</a><br>
Homepage: <a href="http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert" target="_blank">http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert</a><br>
<br>
Tel.: +49 - (0)711 - 68563613<br>
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