[gmx-users] RMSD with Vsite vs No Vsites

[Peter C. Lai]

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...

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