well the deviations are about more than 0.5 nm.. On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai <p...@uab.edu> wrote:
> On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote: > > Hi > > > > 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. > > > > I once again checked my Vsites definitions and set up, there doesnt seem > to be any error in definition as per my understanding. > > > > Is there any other reason that may be causing the mismatch? Or I may have > done something wrong in the setting up Vsites simulations. > > > > thanks > > sikandar > > how large are the RMSD deviations? are they statistically significant for > your needs? (i.e. if you only are about 1A scales, then RMSD differences > < 0.05nm would be meaningless... > > -- > =============================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | BEC 257 > Genetics, Div. of Research | 1150 10th Avenue South > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > =============================================================== > >
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