[gmx-users] RMSD with Vsite vs No Vsites

[Mark Abraham]

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?

Mark

>
> 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
>     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 <mailto:pcl at uab.edu>                  | Birmingham AL
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>     ===============================================================
>
>

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