[gmx-users] RMSD with Vsite vs No Vsites
Peter C. Lai
pcl at uab.edu
Fri May 6 08:49:32 CEST 2011
On 2011-05-05 11:21:54AM -0500, Sikandar Mashayak wrote:
> 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.
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
pcl at uab.edu | Birmingham AL 35294-4461
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