[gmx-users] RMSD with Vsite vs No Vsites

[Mark Abraham]

On 6/05/2011 2:21 AM, 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.

GROMACS simulations are not intrinsically reproducible... 
http://www.gromacs.org/Documentation/Terminology/Reproducibility

Mark