[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:
> Thanks.
> 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 
> could,
>    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 
> 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 <<==

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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