[gmx-users] RMSD with Vsite vs No Vsites
symashayak at gmail.com
Fri May 6 09:32:55 CEST 2011
well the deviations are about more than 0.5 nm..
On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai <pcl at 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
> > 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
> pcl at uab.edu | Birmingham AL 35294-4461
> (205) 690-0808 |
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