<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
<title></title>
</head>
<body>
Hi Nicolas,<br>
<br>
did you switch on com-correction for translation? (comm-mode = linear)<br>
perhaps all the (internal) energy of your system is transformed into
translation, and your system is currently rushing thru interstellar
space...<br>
<br>
Cheers, Lars<br>
<br>
David van der Spoel wrote:<br>
<blockquote cite="mid1086693859.22511.47.camel@localhost.localdomain"
type="cite">
<pre wrap="">On Tue, 2004-06-08 at 12:16, nicolas Dinter wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear David,
See the atached file: msd.jpg.
That's doesn't look like as a liquid.
</pre>
</blockquote>
<pre wrap=""><!---->It's freezing indeed...
How about energies and temperatures?
</pre>
<blockquote type="cite">
<pre wrap="">Thank you.
Nicolas Dinter
-----Original Message-----
From: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
[<a class="moz-txt-link-freetext" href="mailto:gmx-users-bounces@gromacs.org">mailto:gmx-users-bounces@gromacs.org</a>]On Behalf Of David van der Spoel
Sent: mardi 8 juin 2004 18:49
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] liquid?
On Tue, 2004-06-08 at 07:34, nicolas Dinter wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Dear Gromacs users,
I have done a NPT simulation for the Benzene (120 molecules/ 1bar/ 300K).
</pre>
</blockquote>
<pre wrap="">I
</pre>
<blockquote type="cite">
<pre wrap="">optain good values for box size and density but when I have a look in the
ngmx animation, benzene seems to be solid! Moreover, from this point, if I
increase the Temperature and the pressure to 673K and 150 bar there is not
change for the box-size and molecules just vibrate.
If there somebody who can explain me why?
</pre>
</blockquote>
<pre wrap="">Are you looking at the right stuff? Check the diffusion using g_msd...
</pre>
<blockquote type="cite">
<pre wrap="">thanks.
nicolas dinter.
_______________________________________________
gmx-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
</pre>
</blockquote>
<pre wrap="">--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4205 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a class="moz-txt-link-abbreviated" href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a class="moz-txt-link-freetext" href="http://xray.bmc.uu.se/~spoel">http://xray.bmc.uu.se/~spoel</a>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
______________________________________________________________________
_______________________________________________
gmx-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
</pre>
</blockquote>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
*******************************************************
Lars Schäfer
MPI for biophysical Chemistry
Theoretical and computational Biophysics group
Department 070
Am Fassberg 11, D-37077 Goettingen
Tel: 0049 551 201-2305, Fax: 0049 551 201-2302
E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:Lars.Schaefer@mpi-bpc.mpg.de">Lars.Schaefer@mpi-bpc.mpg.de</a>
Home: <a class="moz-txt-link-freetext" href="http://wwwuser.gwdg.de/~lschaef2/homepage.html">http://wwwuser.gwdg.de/~lschaef2/homepage.html</a>
*******************************************************</pre>
</body>
</html>