[gmx-users] Projecting conformational changes onto PCs

[rmendez]

Hi Tsjerk,

Thanks for your answer, but g_anaeig (among other things) gives the
projection of each snaphot of my trajectory onto the selected PCs along
time. What I want is the projection of a different structure, for instance
the difference between my protein into a closed conformation (different from
the open conformation that I used in the MD simulations). Ideally I would
have a Delta_R vector (3N vector) after superposing conformation 2 onto 1.
This is the vector I would like to project onto the first N PCs, so the
projections would tell me how much each PCs contribute to the observed
conformational change. I guess there is no tool to do that on gromacs
(although there are all the ingredients needed), is there ?

Thanks,

Raul

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