<!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 bgcolor="#ffffff" text="#000000">
Hi Berk,<br>
<br>
I used weak berendsen temperature coupling with tau_t = 0.1 and a ref_t
of 298.15 K. My average temperature during the NPT run (disregarding
the first 100 ps) is ca. 298.20 K (as given by g_energy).<br>
I had another question to you, Berk, in my last mail to the list maybe
two hours ago, regarding your Orientation Restraints algorithm. Have
you seen this or should I repost it?<br>
<br>
Best regards,<br>
<br>
Andreas<br>
<br>
<br>
Berk Hess wrote:<br>
<blockquote cite="midBLU134-W3362FDCC2746765499E26E8E080@phx.gbl"
type="cite">
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
FONT-SIZE: 10pt;
FONT-FAMILY:Tahoma
}
</style>
<div style="text-align: left;"><br>
</div>
<br>
<br>
<br>
<hr id="stopSpelling">> Date: Wed, 12 Mar 2008 12:31:12 +0100<br>
> From: <a class="moz-txt-link-abbreviated" href="mailto:andreas.frank@ch.tum.de">andreas.frank@ch.tum.de</a><br>
> To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Subject: [gmx-users] Re: DMSO G53a6 FF in Gromacs<br>
> <br>
> Hi Berk,<br>
> <br>
> Thanks for replying so quick. I made it rigid in that way that I
used <br>
> bonded interactions also for the groups that are not directly
connected <br>
> (FF parameters gb_49 & gb_50) and then applied all-bond SHAKE.
For the <br>
> other bonds I used gb_41, gb42 and for the three angles ga_45 and
ga_46.<br>
> <br>
> Andreas<br>
<br>
There could be another issue.<br>
With reaction-field you always introduce integration errors.<br>
With water this leads to a temperature of 305 K when Berendsen coupling<br>
to 300 K with tau_t=0.1 ps and the Gromos cut-off setup.<br>
<br>
In Gromos there is/was a problem with inconsistent ways of determining<br>
the temperature. Therefore the effective temperature in the simulation<br>
can be several degrees higher than the one reported in the paper.<br>
<br>
What coupling method did you use and what is your real temperature?<br>
<br>
Berk.<br>
<br>
<br>
<hr>Express yourself instantly with MSN Messenger! <a
href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/"
target="_new">MSN Messenger</a>
<pre wrap="">
<hr size="4" width="90%">
_______________________________________________
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>
<div class="moz-signature">-- <br>
<br>
</div>
</body>
</html>