On 6/05/2011 5:32 PM, Sikandar Mashayak wrote:
well the deviations are about more than 0.5 nm..
And what does gmxcheck -s1 -s2 show? Mark
On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai <p...@uab.edu <mailto: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 <mailto:p...@uab.edu> | Birmingham AL 35294-4461 (205) 690-0808 <tel:%28205%29%20690-0808> | ===============================================================
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