<div dir="ltr"><div>Thanks.</div>
<div>FYI - I was already subsribed when I tried to post, the reply I got from <a href="mailto:gmx-developers-bounces@gromacs.org">gmx-developers-bounces@gromacs.org</a> :</div>
<div>The results of your email command are provided below. Attached is your<br>original message.</div>
<div>- Results:<br> Ignoring non-text/plain MIME parts</div>
<div>- Unprocessed:<br> I would your help on how to do the following:<br> I have a 2-body interaction, which I have defined in the file<br> "topology.top", under the tag "[ pairs ]".<br> I would like to, during the simulation itself, to generate a new file, that<br>
for each frame will tell me:<br> (1) Fraction of intact 2-bodies. [ defining intact is not an issue; I could,<br> for example, use a geometric criterion, or something similar ].<br> (2) Current total energy, and energy parts.<br>
Now, I am familiar with C language, and not afraid of modifying the source<br> code.<br> ==>> I will appreciate your help with telling me in what files.c and which<br> function & variables do the coordinates and energies are stored and<br>
defined <<==<br> As for the actual printing, I believe that I could simply output my stuff<br> after the function "write_xtc_traj" is called.<br> Your help is highly appreciated! Omer Markovitch.<br>
Koby Levy research group,<br> Weizmann Institute of Science.<br> <a href="http://www.weizmann.ac.il/sb/faculty_pages/Levy/">http://www.weizmann.ac.il/sb/faculty_pages/Levy/</a></div>
<div>- Done.</div>
<div><br clear="all"> <br>Koby Levy research group,<br>Weizmann Institute of Science. <br><a href="http://www.weizmann.ac.il/sb/faculty_pages/Levy/">http://www.weizmann.ac.il/sb/faculty_pages/Levy/</a><br><br><br></div>
<div class="gmail_quote">On Sun, Sep 7, 2008 at 15:40, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="Ih2E3d"><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>Could you please refer me to the proper resource, about gromacs.<br>I have tried to post the following question in gromacs-developer list,<br>
but could not post there:<br>[in short - i am asking where do the energy & coordinates variables are<br>defined & printed]<br><br>========================================<br>Hello,<br>I would your help on how to do the following:<br>
<br>I have a 2-body interaction, which I have defined in the file<br>"topology.top", under the tag "[ pairs ]".<br>I would like to, during the simulation itself, to generate a new file,<br>that for each frame will tell me:<br>
(1) Fraction of intact 2-bodies. [ defining intact is not an issue; I<br>could, for example, use a geometric criterion, or something similar ].<br></blockquote><br></div>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.
<div class="Ih2E3d"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">(2) Current total energy, and energy parts.<br></blockquote><br></div>I don't understand what you mean (apart from what is defined already e.g. using energy groups).
<div class="Ih2E3d"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><br>Now, I am familiar with C language, and not afraid of modifying the<br>source code.<br>==>> I will appreciate your help with telling me in what files.c and<br>
which function & variables do the coordinates and energies are stored<br>and defined <<==<br>As for the actual printing, I believe that I could simply output my<br>stuff after the function "write_xtc_traj" is called.<br>
<br>Your help is highly appreciated! Omer Markovitch.<br>========================================<br><br>Koby Levy research group,<br>Weizmann Institute of Science.<br><a href="http://www.weizmann.ac.il/sb/faculty_pages/Levy/" target="_blank">http://www.weizmann.ac.il/sb/faculty_pages/Levy/</a><br>
<br><br>On Mon, Sep 1, 2008 at 14:03, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a><br><mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>> wrote:<br>
<br> <br></blockquote><br></div>
<div>
<div></div>
<div class="Wj3C7c">-- <br>David van der Spoel, Ph.D., Professor of Biology<br>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org" target="_blank">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se</a><br>
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