[gmx-users] RMSD with Vsite vs No Vsites
Mark.Abraham at anu.edu.au
Fri May 6 10:13:10 CEST 2011
On 6/05/2011 5:32 PM, Sikandar Mashayak wrote:
> well the deviations are about more than 0.5 nm..
And what does gmxcheck -s1 -s2 show?
> On Fri, May 6, 2011 at 1:49 AM, Peter C. Lai <pcl at uab.edu
> <mailto: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 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
> < 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 <mailto:pcl at uab.edu> | Birmingham AL
> (205) 690-0808 <tel:%28205%29%20690-0808> |
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