[gmx-users] Shell dynamics with vdW terms.

Tue Jun 9 16:29:39 CEST 2009

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