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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
