hello all,
I'am performing a 1000ns simulation for my protein and want to observe it's dynamic motion of domains through PCA analysis. i have two questions:
1) do we have to remove the PBC conditions and fit the protein before going for gmx_covar ?
2) how to lsq fit the protein ligand complex and calculate its covariance, as ligand structure distorts everytime while getting the average structure ?
Ahmad Al Khraisat sir i have another doubt, what atoms should we focus on while making the covariance matrix? should it be backbone or C-alpha or protein?
Next, you can perform the lsq fit of the protein-ligand complex using the gmx rms tool with the -fit option, and then use the gmx_covar tool to calculate the covariance matrix of the complex.
If the ligand structure distorts every time while getting the average structure, you may need to perform multiple simulations or use an ensemble-based approach to obtain a more accurate representation of the protein-ligand complex.
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