[gmx-users] Normal Mode Analysis

James Starlight jmsstarlight at gmail.com
Thu Nov 10 08:51:11 CET 2011

Hi Tsjerk,

Thanks for help. So as I understood if I want to calculate fluctuations
only for Calpha I must first to do NMA of my reference in some mode
subspace consisted of the eigenvectors for Calpha atoms only. Does this
correct ?
Previously I've done something like this for random subspace of modes in
MMTK (just to reduce the space for calculation) but how perform such
operation in Gromacs I havent known yet :)

The c-alphas are less hindered in the second model due to the absence
> of the side chains and such. There's just more freedom.
It's known that solevnt for instance could significant damp motions from
normal modes. So in my case It seems that sidechains act as the solvent.
How do you think may sidechains not only damp motions oberved for C-alpha
atoms merely but also change the trajectory of their motion?

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