<div dir="ltr"><div>OK,</div>
<div>For my protein, a native contact within 2 residues or 2 atoms is defined according to the CSU algorithm. In other words - for each native contact, I have its sigma - the minimum distance, taken from the PDB file.</div>
<div>With that sigma, I have defined, for each contact, a Lennard-Jones force. I have added this force in the topology file.</div>
<div>Now, DURING the simulation, I would like to know how many of these contacts are still intact, that is - how many contacts obey, say, to a distance of 1.5*sigma.</div>
<div> </div>
<div>Now, I could do this analysis by taking a trajectory file that Gromacs has already outputed, but I think its neater if I'll do this DURING the simulation.</div>
<div>Meaning I want to add to the source code a function that will receive a list of my sigma_per_contact, and will output the fraction of native contacts that currently obey 1.5*sigma.</div>
<div>Additionally, I would like to print the relevant energies, so I could use the WHAM algorithm.</div>
<div> </div>
<div>You help is appreciated. Omer Markovitch.<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 20:01, 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">Omer Markovitch wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thanks.<br>FYI - I was already subsribed when I tried to post, the reply I got from <a href="mailto:gmx-developers-bounces@gromacs.org" target="_blank">gmx-developers-bounces@gromacs.org</a> <mailto:<a href="mailto:gmx-developers-bounces@gromacs.org" target="_blank">gmx-developers-bounces@gromacs.org</a>> :
<div class="Ih2E3d"><br>The results of your email command are provided below. Attached is your<br>original message.<br>- Results:<br> Ignoring non-text/plain MIME parts<br>- 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></div></blockquote><br>
It would be easier to help you if you defined the problem somewhat more.
<div class="Ih2E3d"><br><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"> 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><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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