Hi All, I have a question/confusion regarding interpolate frames option '-nframes' in gmx anaeig.
One can find the extreme conformations as dot products projected on a selected eigenvector (to simplify say first eigenvector PC1). As the manual says, with -nframes (in anaeig) one can interpolate between the two extremes. I am confused with 'interpolating' here: a) Are these interpolated frames, between extremes, the 'real' conformations extracted from the trajectory? Which in that case one cannot define nframes > total frames falling between the extremes (dot product projections min and max on selected eigenvector). I don't think am right here because I could simply use a filtering option in anaeig. Or b) Are these interpolated smoothened frames some kind of predicted conformations along a path? In that case these interpolated conformations cannot be considered as 'real' conformational changes (that is they are not extracted from the trajectory) occurring between the extremes. Many times people show beautiful animations (interpolations between extremes), then they are not true conformational changes extracted from the trajectory. In that case I should not trust their visual explanations about the conformational changes. But I believe, please correct me, the interpolation is done using some intermediate real frames extracted from the trajectory otherwise it will not look so smooth. I hope I was able to ask my source of confusion clearly. Thanks Dave -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
