[gmx-developers] [Fwd: Re: Water Kinetics]
David van der Spoel
spoel at xray.bmc.uu.se
Sun Sep 7 19:01:55 CEST 2008
Omer Markovitch wrote:
> FYI - I was already subsribed when I tried to post, the reply I got from
> gmx-developers-bounces at gromacs.org
> <mailto:gmx-developers-bounces at gromacs.org> :
> The results of your email command are provided below. Attached is your
> original message.
> - Results:
> Ignoring non-text/plain MIME parts
> - Unprocessed:
> 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
> for example, use a geometric criterion, or something similar ].
> (2) Current total energy, and energy parts.
> Now, I am familiar with C language, and not afraid of modifying the
> ==>> I will appreciate your help with telling me in what files.c and
> function & variables do the coordinates and energies are stored and
> defined <<==
It would be easier to help you if you defined the problem somewhat more.
> 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.
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
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