[gmx-users] Shell dynamics with vdW terms.

Wed Jun 10 08:42:26 CEST 2009

On Tuesday 09 June 2009 18:27:16 Berk Hess wrote:
> > From: rafapa at us.es
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Shell dynamics with vdW terms.
> > Date: Tue, 9 Jun 2009 16:29:39 +0200
> >
> > On Tuesday 09 June 2009 10:02:47 Berk Hess wrote:
> > > Hi,
> > >
> > > The equation you refer to is only an initial guess for the
> > > optimization. The positions of the shells are optimized using the
> > > forces from the full potential function.
> > >
> > > Berk
> > >
> > > > From: rafapa at us.es
> > > > To: gmx-users at gromacs.org
> > > > Date: Tue, 9 Jun 2009 09:51:13 +0200
> > > > Subject: [gmx-users] Shell dynamics with vdW terms.
> > > >
> > > > Hello,
> > > >
> > > > I have some troubles understanding the way used by Gromacs in
> > > > optimizing the position of shells. In section 3.5.1 the manual says
> > > > that the force on a shell particle is decomposed into two terms. The
> > > > first represents the polarization and the second includes the Coulomb
> > > > and van der Waals interactions. It continues assuming that the second
> > > > term is constant and derives an analytic expression to calculate the
> > > > shell position.
> > > >
> > > > My troubles arise after reading the paper: J. Phys. Chem. B 2009,
> > > > 113, 7270-7281 by A. Villa, B. Hess & H. Saint-Martin. In the paper
> > > > they simulate Lanthanides in water. In Table 2 they assign a 1/r**12
> > > > term to the ion-shell - water-shell interaction (the A_MIM
> > > > parameter). I believe that this term is used in eq. 8 of the
> > > > Supporting Information. Because is vdW like it seems to me that it
> > > > breaks the previously mentioned assumption of vdW constancy.
> > > >
> > > > Could anybody help me?
> > > >
> > > > Thanks a lot.
> > > >
> > > > Rafael
> > > >
> > > > --
> > > > Dr. Rafael R. Pappalardo
> > > > Dept. of Physical Chemistry, Univ. de Sevilla (Spain)
> > > > e-mail: rafapa at us.es
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> > Dear Berk,
> >
> > thanks for the quick answer.
> >
> > I am having lot of troubles trying to minimize a cation+1 water molecule
> > using Gromacs 4.0.5. The minimization proceeds without warnings but at a
> > certain point it seems that the shell minimizer does not work ok. The
> > kind of structures I am obtaining are:
> > Generated by trjconv : Cf in Water t=   9.00000
> >     6
> >     1Cf_s    Cf    1   1.49566   1.61167   1.73228
> >     1Cf_s    Ms    2   1.49450   1.62107   1.72892
> >     2SOL     OW    3   1.51913   1.41088   1.80113
> >     2SOL    HW1    4   1.51596   1.36681   1.89843
> >     2SOL    HW2    5   1.53786   1.31814   1.75093
> >     2SOL     MW    6   1.51789   1.42144   1.79730
> >    3.10740   3.10740   3.10740
> > Generated by trjconv : Cf in Water t=  10.00000
> >     6
> >     1Cf_s    Cf    1   1.49838   1.58947   1.74003
> >     1Cf_s    Ms    2   1.49587   1.60861   1.73299
> >     2SOL     OW    3   1.51772   1.42189   1.79765
> >     2SOL    HW1    4   1.51568   1.37036   1.89631
> >     2SOL    HW2    5   1.53733   1.32238   1.75035
> >     2SOL     MW    6   1.51602   1.43730   1.79166
> >    3.10740   3.10740   3.10740
> > Generated by trjconv : Cf in Water t=  11.00000
> >     6
> >     1Cf_s    Cf    1   1.50510   1.52690   1.75928
> >     1Cf_s    Ms    2   1.50102   1.57015   1.74742
> >     2SOL     OW    3   1.51647   1.43148   1.79236
> >     2SOL    HW1    4   1.51461   1.38178   1.89116
> >     2SOL    HW2    5   1.53582   1.33543   1.74711
> >     2SOL     MW    6   1.50797   1.50425   1.77168
> >    3.10740   3.10740   3.10740
> >
> > I see no warning or error in the md.log file albeit the Coulomb energy is
> > rather large. The run continues at to t=50.000 with the message:
> >
> > Stepsize too small, or no change in energy.
> > Converged to machine precision,
> > but not to the requested precision Fmax < 0.1
> >
> > Could I sent you the input files in order to get some advice?
> >
> >
> > Best regards,
> >
> > Rafael
> >
> > --
> > Dr. Rafael R. Pappalardo
> > Dept. of Physical Chemistry, Univ. de Sevilla (Spain)
> > e-mail: rafapa at us.es
>
> At this point I have no clue if there might be something wrong at all.
> There are many questions to ask:
> What energies would you expect?
> Have you checked if the minimized structure looks reasonable?

Yes, I have checked the structures. During the minimization the charges on the 
cation nucleus and the mobile charge on the oxygen collapse.

> Is this a force field from the literature that it proven to work with this
> water model? Polarizable models are tricky, if there is not enough
> repulsion or the spring constant is too weak you can easily get a
> polarization catastrophe.
>
> Berk
>

The force field is an in house development. We have tried the minimization 
using DL-POLY and a Monte Carlo code and the final result seems sensible. The 
troubles are with Gromacs. We have checked that the initial energy is the same 
between Gromacs and DL-POLY.

Thanks again.

>
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-- 
Dr. Rafael R. Pappalardo
Dept. of Physical Chemistry, Univ. de Sevilla (Spain)
e-mail: rafapa at us.es