Justin,<br><br>the main problem is the my simulation in nvt ensemble :) I understand that density is constant in that conditions but I'd like to find way to check this values for different components of my system.<br><br>
<br>James<br><br><div class="gmail_quote">2012/5/28 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="HOEnZb"><div class="h5"><br>
<br>
On 5/28/12 3:09 PM, James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Dear Gromacs users!<br>
<br>
<br>
In this task I have two systems:<br>
<br>
First system consist of single layer of Ccl4 molecules.<br>
<br>
Second system consist of membrane-mimicking layer of Ccl4 surrounded by water<br>
and the protein embedded in that biphastic layer.<br>
<br>
I'd like to measure density in both of my systems to check of its packing<br>
degree. How could I do it in the case of homo system- (where I'd like to check<br>
density in the Ccl4 layer only) as well as in more complex hetero system (<br>
where I'd like to check density in each layer separately as well as compute<br>
averaged density among all layers) ?<br>
<br>
<br>
</blockquote>
<br></div></div>
The density of the homogeneous system can easily be obtained from the .edr file, as long as the ensemble was NPT. With NVT, the density term is not written, IIRC.<br>
<br>
In the case of the heterogeneous system, use g_density to obtain partial densities as a function of box dimension.<br>
<br>
-Justin<span class="HOEnZb"><font color="#888888"><br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</font></span></blockquote></div><br>