[gmx-users] potential across surface

[Andre Farias de Moura]

hi david,

I've checked both and don't think this is the problem,
the density profile shows an interfacial region less
than 0.5 nm thick and there is no overall movement.

my simulation system contains a 6.0 nm water slab in a
50 nm box (z direction), I'm sending you my potential
files to clarify what I mean. I got these files using:

g_potential -f water.xtc -s water.tpr -n index.ndx -sl 50

thanks again,

andre'


/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

    Dr. Andre' Farias de Moura

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

  Laboratorio de Quimica Teorica
Universidade Federal de Sao Carlos
     Sao Carlos - SP - Brasil

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

        Endereco Atual

    Grupo de Quimica Quantica
Instituto de Quimica de Sao Carlos
    Universidade de Sao Paulo
    Sao Carlos - SP - Brasil
    Telefone: 55-16-3373-8055

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

On Thu, 5 Aug 2004, David van der Spoel wrote:

> On Wed, 4 Aug 2004, Andre Farias de Moura wrote:
>
> >
> >dear gmx-users,
> >
> >I tried to use g_potential to get the potential
> >across air-water interface but I'm not sure
> >about the meaning of potential.xvg output. I
> >expected something like a nearly constant value
> >in bulk water region followed by a steep drop
> >in the interfacial region, but got instead a
> >steadly increasing function with only slight
> >changes across the interface.
> >
> >is that what g_potential should give me?
> >
> >how could I get a potential difference from
> >such plot?
>
> Have you checked how well-defined your interface is (use g_density)?
>
> Is your water slab moving? (remove center of mass motion)
> >
> >thanks in advance,
> >
> >andre'
> >
> >/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> >
> >    Dr. Andre' Farias de Moura
> >
> >/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> >
> >  Laboratorio de Quimica Teorica
> >Universidade Federal de Sao Carlos
> >     Sao Carlos - SP - Brasil
> >
> >/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> >
> >        Endereco Atual
> >
> >    Grupo de Quimica Quantica
> >Instituto de Quimica de Sao Carlos
> >    Universidade de Sao Paulo
> >    Sao Carlos - SP - Brasil
> >    Telefone: 55-16-3373-8055
> >
> >/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> >
> >_______________________________________________
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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