[gmx-users] Re: Essential dynamics

bharat gupta bharat.85.monu at gmail.com
Tue Feb 1 05:55:31 CET 2011


I have simulated (3ns) the crystal str of GFP (pdb -1GFL, without
chromophore formation) and a modeled variant of GFP with a change in loop
region (loop length is extended) . After calculating the RMSD of both strs.
and superimposing reveals that RMSD doesnot fluctuate much for the modeled
str (though it doesnot exactly superimpose on the RMSD of the crystal str of
GFP) . I want to carry out Essential dynamics of both the structure and want
to locate which region shows minimal and maximal amplitudes of motion (ie.
whats the cause of this fluctuation) ... i need help in this regard ??

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