[gmx-users] Projecting conformational changes onto PCs

Dear all, Is there any gromacs tool to project a given conformational change (i.e. the structural difference after superposing a given protein in conformation 1 onto conformation 2), on a set of already computed Principal components computed by g_covar? Or should I implement myself ? I would

Re: [gmx-users] Projecting conformational changes onto PCs

g_anaeig Cheers, Tsjerk On Tue, Apr 1, 2014 at 9:36 PM, Mendez Giraldez, Raul rmen...@email.unc.edu wrote: Dear all, Is there any gromacs tool to project a given conformational change (i.e. the structural difference after superposing a given protein in conformation 1 onto conformation

Re: [gmx-users] Projecting conformational changes onto PCs

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

Re: [gmx-users] Projecting conformational changes onto PCs

Hi Raul, The answer to a question with 'projection' and 'eigenvector' is g_anaeig. But you project a structure, not a difference vector. You can also calculate the inner product between two sets of eigenvectors, or between a delta vector and a set of eigenvectors, again using g_anaeig (-inpr). I