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

[Omer Markovitch]

Thanks.
FYI - I was already subsribed when I tried to post, the reply I got from
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 <<==
   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/
- Done.


Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Sun, Sep 7, 2008 at 15:40, David van der Spoel <spoel at xray.bmc.uu.se>wrote:

>
>
>> 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 though.
>
> (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
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-developers-request at gromacs.org.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20080907/ce666341/attachment.html>