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On 6/04/2012 4:57 PM, Acoot Brett wrote:
<blockquote
cite="mid:1333695461.92132.YahooMailNeo@web121804.mail.ne1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:times
new roman, new york, times, serif;font-size:12pt">
<div>Dear All,</div>
<div> </div>
<div>Before and after extention we have 2 trajectorty files, and
by trjcat we got we, then we can do the g_rms</div>
<div> </div>
<div>g_rms -s *.tpr -f *_noPBC.xtc -o rmsd.xvg -tu ns</div>
<div> </div>
<div>But here for the g_rms command I find no matter whether we
use the *.tpr of the initiation of the production MD, or the
*.tpr for the initiation of the extension part, the rmsd.xvg
curves seems same.</div>
<div> </div>
<div>Will you please give some comment on it?</div>
</div>
</blockquote>
<br>
If you used tpbconv -extend, or similar, then the two .tpr files
contain the same structure, and so the reference structure for g_rms
is the same. The starting configuration for MD is determined by the
contents of the -cpi file, if given, and the .tpr file only as a
fallback.<br>
<br>
Mark<br>
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