GROMACS version:
GROMACS modification: Yes/No
Several discussions on the forum are dedicated to the topic of running pca and fel in gromacs. But I still has several questions and would be grateful for your help:
- If there are several proteins with mutations, would it be right to concatenate trajectories (based on Backbone or C-alpha atoms because this groups are identical in size in mutated proteins), then build covariance matrix for concatenated trajectory, then project dots corresponding to different models in concatenated trajectory on the same eigenvector pair, and finally compare regions corresponding to frames from each of mutated models?
- What would be better for FEL analysis: plot one graph for concatenated trajectory and distinguish regions that correspond to frames from each of mutated models, OR plot several FEL graphs, each for one of the mutated models and then compare them?