<meta charset="utf-8"><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><br><div class="gmail_quote">
On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu">pcl@uab.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><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>
</div></div>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>
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