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For a homogenious system, you can also use g_density: g_density -sl 1
-dens mass -f -s -o<br>
<br>
Mark Abraham wrote:
<blockquote cite="mid:fbcec90f2e253.4cb4ed14@anu.edu.au" type="cite">
<pre wrap="">You get the density by running g_energy. If you've tried that and seen that the density wasn't there, that would be because your volume is constant in an NVT simulation. grompp probably reported the density when you made the .tpr, however.
Mark
----- Original Message -----
From: <a class="moz-txt-link-abbreviated" href="mailto:vferrario@units.it">vferrario@units.it</a>
Date: Tuesday, October 12, 2010 23:14
Subject: Re: [gmx-users] g_density options
To: <a class="moz-txt-link-abbreviated" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
</pre>
<blockquote type="cite">
<pre wrap="">Thanks a lot, but... How can I exctract density information by
using g_energy?
Valerio
"Justin A. Lemkul" <a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a> ha scritto:
</pre>
<blockquote type="cite">
<pre wrap="">
Justin A. Lemkul wrote:
</pre>
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<pre wrap="">
<a class="moz-txt-link-abbreviated" href="mailto:vferrario@units.it">vferrario@units.it</a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">I'm a GROMACS user and I want to authomatize solvent
</pre>
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</blockquote>
</blockquote>
<pre wrap="">parametrization in
</pre>
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<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">GROMOS force-field. The parametrization of a solvent converg
</pre>
</blockquote>
</blockquote>
</blockquote>
<pre wrap="">also on
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">the density. The problem is that g_density always ask on
</pre>
</blockquote>
</blockquote>
</blockquote>
<pre wrap="">which element
</pre>
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<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">of the system compute the density and it is waiting for a
</pre>
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</blockquote>
</blockquote>
<pre wrap="">replay that
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">I can't authomatize. Is it possible to set the g-density
</pre>
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</blockquote>
<pre wrap="">calculation>>>on the whole system by default and skippink the
choice step?
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">If you're analyzing a homogeneous liquid system, then
</pre>
</blockquote>
</blockquote>
<pre wrap="">g_density is the wrong tool. It calculates density as a
function of the box vector. The whole density of the
system is written to the .edr file and can be extracted using
g_energy.>>
</pre>
<blockquote type="cite">
<pre wrap="">And if you're looking to automate any process in Gromacs, see
</pre>
</blockquote>
<pre wrap="">the following:
</pre>
<blockquote type="cite">
<pre wrap=""><a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/How">http://www.gromacs.org/Documentation/How</a>-
</pre>
</blockquote>
<pre wrap="">tos/Making_Commands_Non-Interactive
</pre>
<blockquote type="cite">
<pre wrap="">-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
<a class="moz-txt-link-freetext" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a>
========================================
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