[gmx-users] Positive Coul. recip. term
Dommert Florian
dommert at icp.uni-stuttgart.de
Wed Feb 29 11:47:03 CET 2012
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
> <dommert at 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
> > <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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--
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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