[gmx-developers] [Fwd: Re: Water Kinetics]

David van der Spoel spoel at xray.bmc.uu.se
Sun Sep 7 14:40:43 CEST 2008

> Could you please refer me to the proper resource, about gromacs.
> I have tried to post the following question in gromacs-developer list,
> but could not post there:
> [in short - i am asking where do the energy & coordinates variables are
> defined & printed]
> ========================================
> Hello,
> I would your help on how to do the following:
> I have a 2-body interaction, which I have defined in the file
> "topology.top", under the tag "[ pairs ]".
> I would like to, during the simulation itself, to generate a new file,
> that for each frame will tell me:
> (1) Fraction of intact 2-bodies. [ defining intact is not an issue; I
> could, for example, use a geometric criterion, or something similar ].

You could define the energy of this new "pair" interaction as binary 1 
or 0 and get the fraction by dividing by the total number of such 
interactions. You may be better off definig this as a bond interaction 

> (2) Current total energy, and energy parts.

I don't understand what you mean (apart from what is defined already 
e.g. using energy groups).

> Now, I am familiar with C language, and not afraid of modifying the
> source code.
> ==>> I will appreciate your help with telling me in what files.c and
> which function & variables do the coordinates and energies are stored
> and defined <<==
> As for the actual printing, I believe that I could simply output my
> stuff after the function "write_xtc_traj" is called.
> Your help is highly appreciated! Omer Markovitch.
> ========================================
> Koby Levy research group,
> Weizmann Institute of Science.
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
> On Mon, Sep 1, 2008 at 14:03, David van der Spoel <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>> wrote:

David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

More information about the gromacs.org_gmx-developers mailing list