[gmx-users] Positive Coul. recip. term
Denny Frost
dsfrost at cableone.net
Wed Feb 29 19:12:34 CET 2012
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.
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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