<br><br><div class="gmail_quote">On Sat, Nov 20, 2010 at 12:54 AM, Sunita Patel <span dir="ltr"><<a href="mailto:sunita@mailhost.tifr.res.in">sunita@mailhost.tifr.res.in</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Dear Users,<br>
<br>
I calculated RMSD for a trajectory with same reference structure using GROMACS<br>
and VMD. I observed completely difference plots for the same data. Please see<br>
the attached file.<br>
<br>
What could be the cause for this disparity?<br></blockquote><div><br></div><div>it is hard to predict what is causing the disparity without what you typed in the terminal, and your system. Perhaps check if you've removed the periodic boundary conditions when calculating the rmsd in gmx by invoking -nopbc option.</div>
<div><br></div><div>Greg</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
Thanks for any suggestion.<br>
<font color="#888888">Sunita<br>
<br>
</font><br>--<br>
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