<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=UTF-8" http-equiv="Content-Type">
<title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
David wrote:
<blockquote
cite="mid1131640752.5334.1.camel@217-208-143-88-o1123.tbon.telia.com"
type="cite">
<pre wrap="">On Fri, 2005-11-11 at 00:17 +0800, Yang Ye wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi, David
I recently met this error with 3.3 version's mdrun.
"More than 12 graph edges per atom (atom xxxx)"
</pre>
</blockquote>
<pre wrap=""><!---->Do you have more than 12 bonds for a single atom?
</pre>
</blockquote>
I noticed that in the md.log<br>
<br>
Max number of graph edges per atom is 8<br>
-------------------------------------------------------<br>
Program mdrun_s_mpi, VERSION 3.3<br>
Source code file: mshift.c, line: 95<br>
Fatal error:<br>
More than 12 graph edges per atom (atom 2256)<br>
<br>
Seems a bug in mdrun...<br>
<blockquote
cite="mid1131640752.5334.1.camel@217-208-143-88-o1123.tbon.telia.com"
type="cite">
<pre wrap="">
</pre>
<blockquote type="cite">
<pre wrap="">My system is a 8-atom stable structure, each of them is bonded and these
bonds are transformed to SHAKE constraints. The system is
over-constrained with 28 bonds. The error applied to almost each one of
them. I did not meet this error with a pre-3.3 cvs version. Is there any
workaround to lift this limit?
</pre>
</blockquote>
<pre wrap=""><!---->Not that I know of. In addition you should verify that you have any
degrees of freedom left: 8x3 is 24, so your system should have -4
degrees of freedom.
</pre>
</blockquote>
It shows 0 for the DOF of that group in grompp output. So I think that
it is okay.<br>
<blockquote
cite="mid1131640752.5334.1.camel@217-208-143-88-o1123.tbon.telia.com"
type="cite">
<blockquote type="cite">
<pre wrap="">Thanks.
</pre>
</blockquote>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<i>Regards,</i><br>
Yang Ye<br>
<small><i>Computational Biology Lab<br>
School of Biological Sciences<br>
Nanyang Technological University<br>
Singapore<br>
Tel: 6316-2884<br>
</i></small>
</div>
</body>
</html>