[gmx-users] Positive Coul. recip. term
Dommert Florian
dommert at icp.uni-stuttgart.de
Sat Feb 25 12:43:30 CET 2012
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
> <dommert at 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
> > --
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>
> --
> Florian Dommert
> Dipl. - Phys.
>
> Institute for Computational Physics
> University Stuttgart
>
> Pfaffenwaldring 27
> 70569 Stuttgart
>
> EMail: dommert at 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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--
Florian Dommert
Dipl. - Phys.
Institute for Computational Physics
University Stuttgart
Pfaffenwaldring 27
70569 Stuttgart
EMail: dommert at 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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