<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 29/05/2012 3:21 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopzF7ZN+mV3NLCA0T9=zZUiA0jKx70pSXLJypq5M3y9qhQ@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
AFAIK, there's no easy way to do that with GROMACS tools. The
problem lies in defining the shape over which you want to compute
such a partial density, since you need to compute its volume. Any
solution is likely to be at least a bit crude, even for a trivial
case of a membrane-mimic in water whose interfaces are roughly
orthogonal to a box vector.<br>
<br>
g_select may be useful in forming a suitable subset, and g_sas may
be suitable for computing density and/or volume.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopzF7ZN+mV3NLCA0T9=zZUiA0jKx70pSXLJypq5M3y9qhQ@mail.gmail.com"
type="cite"><br>
<br>
James<br>
<br>
<div class="gmail_quote">2012/5/28 Justin A. Lemkul <span
dir="ltr"><<a moz-do-not-send="true"
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>
========================================<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/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 moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></span></blockquote>
</div>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>