[gmx-users] Reference structure for g_covar

[vivek modi]

Hi,

I am doing Essential Dynamics on a protein (150 residues). The simulation is
100ns long and the RMSD becomes very stable after 25ns.
I have gone through the mailing list archives but could not find a precise
answer to the following question.

When I calculate the cosine content for the first PC by taking the average
structure for fitting using g_covar it gives a very high value ~.8.
But when I change the reference structure to the starting structure then I
get a cosine value ~.1.

I also repeated the same by dividing my trajectory into two equal halves but
the cosine value with average structure as a reference is always very high
while it is reasonably low with starting structure taken as reference.

My question is why the cosine content is dependent on the fitting
structure used in g_covar?  And, especially, which structure is
recommended to use in Essential Dynamics analysis ?

Any help is appreciated.


Thanks a lot.


Regards,

Vivek Modi
Graduate Student,
IITK.
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