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<br />On Sat, 20 Nov 2010 01:13:51 -0500, Yongchul Chung wrote
<br />> 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 style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;" class="gmail_quote">
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>
<br />>
<br />> 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.
<br />
<br />Still, am getting the same plot in gmx even after removal of periodic boundary conditions. Visual observation of trajectory on VMD is more similar to the RMSD am getting from VMD. My worry is that why gmx is not giving the similar result.
<br />
<br /></font><font size="2">Thanks Greg.
<br />Any suggestion will be appreciated.
<br />Sunita
<br /></font><font size="2">>
<br />> Greg
<br />> <blockquote style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;" class="gmail_quote">
<br />>
Thanks for any suggestion.
<br />>
<font color="#888888">Sunita
<br />>
<br />>
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</blockquote>
<br />
<br />
<br />Dr. Sunita Patel
<br />
---------------------------------------------
<br />
Visiting Fellow
<br />
Department of Chemical Sciences
<br />
T.I.F.R., Homi Bhabha Road, Colaba
<br />
Mumbai - 400005
<br />
---------------------------------------------
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