[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]
> 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.
> 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
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