[gmx-users] Re: 3D-density
tsjerkw at gmail.com
Thu Feb 1 13:18:09 CET 2007
> 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
Maybe if I have time somewhere I will combine the functionality. But not now.
> Once more thanks for your help!
> 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
3584 CH Utrecht
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