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On 6/05/2011 5:32 PM, Sikandar Mashayak wrote:
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cite="mid:BANLkTi=71nq6jQ6UPecn9mznLSH4y64nFg@mail.gmail.com"
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<span class="Apple-style-span" style="border-collapse: collapse;
font-family: arial,sans-serif; font-size: 14px;">well the
deviations are about more than 0.5 nm..</span><br>
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<br>
And what does gmxcheck -s1 -s2 show?<br>
<br>
Mark<br>
<br>
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cite="mid:BANLkTi=71nq6jQ6UPecn9mznLSH4y64nFg@mail.gmail.com"
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On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:pcl@uab.edu">pcl@uab.edu</a>></span>
wrote:<br>
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<div class="h5">On 2011-05-05 11:21:54AM -0500, Sikandar
Mashayak wrote:<br>
> Hi<br>
><br>
> As a test case, I did two simulations one the usual
Protein in Water and other with Vsites at COM of each
monomer but these Vsites dont interact with anyone else. I
was expecting results of these two should match almost
exactly, but when I compare the rmsd for Protein there
seems to be discrepancy.<br>
><br>
> I once again checked my Vsites definitions and set
up, there doesnt seem to be any error in definition as per
my understanding.<br>
><br>
> Is there any other reason that may be causing the
mismatch? Or I may have done something wrong in the
setting up Vsites simulations.<br>
><br>
> thanks<br>
> sikandar<br>
<br>
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how large are the RMSD deviations? are they statistically
significant for<br>
your needs? (i.e. if you only are about 1A scales, then RMSD
differences<br>
< 0.05nm would be meaningless...<br>
<font color="#888888"><br>
--<br>
===============================================================<br>
Peter C. Lai | University of
Alabama-Birmingham<br>
Programmer/Analyst | BEC 257<br>
Genetics, Div. of Research | 1150 10th Avenue South<br>
<a moz-do-not-send="true" href="mailto:pcl@uab.edu">pcl@uab.edu</a>
| Birmingham AL 35294-4461<br>
<a moz-do-not-send="true" href="tel:%28205%29%20690-0808"
value="+12056900808">(205) 690-0808</a> |<br>
===============================================================<br>
<br>
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