Hi I have a done number of MD simulations of a two domain protein with different ligands and also in the apo state. Comparing these simulations I see varying degrees of domain rotation of the one domain relative to the other which I want to quantitatively measure and I was thinking of using DynDom to do this; I have already assessed a number of structures taken from different points throughout the simulations but want a to assess the motion throughout the simulations. >From the user lists I read that I should do ED analysis first. Is this using g_covar and then g_anaeig or using make_edi and then doing ED in mdrun and then assessing these results? Also as the motion appears to be the C-terminal domain relative to the N-terminal domain when using g_covar should I fit over the N-terminal domain backbone but do the analysis over the whole backbone, or just fit over the whole backbone? Also in g_covar is it better for this type of problem to use the -ref option and assess the deviation from the conformation in the structure file instead of from the average? I would appreciate some guidance as although I've read some papers on this subject I am a bit confused as to what is the best way to progress.
Many thanks, Jo.
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