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On 25/11/2011 2:28 AM, Vasileios Tatsis wrote:
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cite="mid:1322148498.38681.YahooMailNeo@web26704.mail.ukl.yahoo.com"
type="cite">
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<div><font class="Apple-style-span" face="verdana, helvetica,
sans-serif" size="2">Dear Gromacs Users,</font></div>
<div><font class="Apple-style-span" face="verdana, helvetica,
sans-serif" size="2"><br>
</font></div>
<div><font class="Apple-style-span" face="verdana, helvetica,
sans-serif" size="2"><span class="Apple-style-span"
style="white-space: pre; ">I am using the -rerun option of
mdrun to re-analyze a trajectory. Thus, I tried to rerun
the same </span></font><span class="Apple-style-span"
style="font-family: verdana, helvetica, sans-serif;
white-space: pre; font-size: 13px; ">trajectory (md.xtc)
with exactly the same md.tpr. </span></div>
<div><span class="Apple-style-span" style="font-family: verdana,
helvetica, sans-serif; white-space: pre; font-size: 13px; ">But
the bonded interactions are not computed or written to the
log file or to the .edr file, resulting to completely
different energy values from the initial log and edr files.</span></div>
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<br>
That does not sound possible if the .tpr is the same. With bond or
angle constraints, some bonded terms would not appear in either
version, of course.<br>
<br>
Mark<br>
<br>
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<pre><font class="Apple-style-span" face="verdana, helvetica, sans-serif" size="2">I am using the following command, in order to read the coordinates stored in the .xtc file and compute the potential energy:</font></pre>
<pre><font class="Apple-style-span" face="verdana, helvetica, sans-serif" size="2">mdrun -rerun md.xtc -s md.tpr
</font></pre>
<pre><font class="Apple-style-span" face="verdana, helvetica, sans-serif" size="2">
</font></pre>
<pre><font class="Apple-style-span" face="verdana, helvetica, sans-serif" size="2">Thanks in advance for your help</font></pre>
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