[gmx-users] Re: 3D-density

[Tsjerk Wassenaar]

Hi Roman,

> But again here I don't know the 3d distribution of anions around
> cations. The reason is to know how much
> anions located around selected ring atoms, chain atoms etc. Maybe g_sdf
> can partially solve the problem.
> Is it possible then plot 3d picture of anions probability around cation?

I think g_sdf would be the most suitable tool to do this. I assume
that you have multiple copies of the cations as well as of the anions.
In that case, using g_density may be quite tedious, unless it's okay
to focus on only one cation and determine distributions around that.
As far as I remember, g_sdf calculates the densities of a selection of
Y molecules around each of a number of X molecules, in your case
meaning that the spatial distribution of anions is determined using
all cations.

Maybe if I have time somewhere I will combine the functionality. But not now.

Cheers,

Tsjerk

>
> Once more thanks for your help!
>
> Sincerely
> /Roman
> P.S. Some time ago I have posted question about MSD and very slow
> dynamics in my system.
> Now I know that this is due to non-polarizable Amber force field (f99)
> used. Unfortunately polarizable one (ff02) is not ported for Gromacs yet
> ...
> -----------------------------------
> Roman Holomb,
> Chalmers University of Technology,
> Göteborg, Sweden.
>
> > Depends on what you really want to do. There is a program g_sdf on the
> > contributions page, which can calculate spatial distribution
> > functions. I have a modified version of g_density (somewhere), which
> > can be used to plot time averaged densities of a given selection. If
> > the latter is what you want, you can contact me off-list.
>
> > Cheers,
>
> > Tsjerk
>
> > On 1/19/07, Roman Holomb <romhol at fy.chalmers.se
> > <http://www.gromacs.org/mailman/listinfo/gmx-users>> wrote:
> > / Dear GROMACS users,
> />/
> />/ I have a question related with 3D-distribution of molecular density
> />/ around a central molecule.
> />/ Is it possible to get such plots from GROMACS trajectory file?
> />/
> />/ Thanks in advance!
> />/
> />/ Sincerely
> />/ /Roman
> /
>
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623