[gmx-users] Positive Coul. recip. term
Dommert Florian
dommert at icp.uni-stuttgart.de
Wed Feb 29 19:49:29 CET 2012
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
> <dommert at 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
> > <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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--
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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