[gmx-users] Shell dynamics with vdW terms.

Berk Hess gmx3 at hotmail.com
Tue Jun 9 18:27:16 CEST 2009 



> 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?
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


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