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? James
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