<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Loris,<br>
<br>
It may be better to have ld_seed=-1. This way, you won't have the same
seed again when you restart.<br>
<br>
@Article{Cerutti2008,<br>
author = "Cerutti, D S and Duke, R and Freddolino, P L and Fan, H and
Lybrand, T P",<br>
title = {Vulnerability in Popular Molecular Dynamics Packages
Concerning Langevin and Andersen Dynamics},<br>
journal = "J Chem Theory Comput",<br>
year = "2008",<br>
volume = "4",<br>
pages = "1669-1680"<br>
}<br>
<br>
Best regards,<br>
Ran<br>
<br>
Loris Moretti wrote:
<blockquote
cite="mid20090311152447.E56AC26311@webmail219.herald.ox.ac.uk"
type="cite">
<pre wrap="">Dear Mark and Oscar,
Thanks for your help!
I checked the velocity distribution and the velocity at different simulation frames. As you said the initial velocities are all set to zero and at the next step are already changed, I also guess by the random thermal noise.
Thus, my idea of simulating the same system with different random generator number for thermal noise (ld_seed) might account for a small variation of the "initial" conditions?
loris...
In message <a class="moz-txt-link-rfc2396E" href="mailto:8c3f24a40903110611j4f69c75emb0f5eef0484de783@mail.gmail.com"><8c3f24a40903110611j4f69c75emb0f5eef0484de783@mail.gmail.com></a> Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a> writes:
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Thus I am a bit confused about it!
</pre>
<pre wrap="">I'm confused about the manual comment about only being meaningful with the
MD integrator, but we 'll have to wait until someone who knows something
about LD can post!
</pre>
</blockquote>
<pre wrap="">
For LD, the velocities will (should) get rescaled by the random thermal
noise, that is- by the Langivin thermostat.
With MD, the thermostat works like friction (positive or negative friction).
So you see, that for LD, an initial velocity of zero should next be changed
by the thermostat, while for MD the rescaling shouldn't work for zero.
--Omer Markovitch.
Koby Levy research group,
Weizmann Institute of Science.
<a class="moz-txt-link-freetext" href="http://www.weizmann.ac.il/sb/faculty_pages/Levy/">http://www.weizmann.ac.il/sb/faculty_pages/Levy/</a>
</pre>
</blockquote>
<pre wrap=""><!---->_______________________________________________
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 search the archive at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!
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>.
Can't post? Read <a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a>
</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: <a class="moz-txt-link-abbreviated" href="mailto:r.friedman@bioc.unizh.ch">r.friedman@bioc.unizh.ch</a>
Skype: ran.friedman
------------------------------------------------------
</pre>
</body>
</html>