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 | =============================================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
