xi zhao wrote: > Dear user: > We know that observing the sampled conformations in the subspace spanned > by the eigenvectors is a so-called two-dimensional projection(2D > projection), in 2-D projection, each point represents a snapshot from > the simulation, and the distribution shows the sampled region along the > first two eigenvectors during the simulation. But I feel confounded, > because I do not know to how to obtain corresponding conformation for > each point in the 2-D projection. Some papers can show these > corresponding conformation. Please help me!
Well, if you're after the original 3N-dimensional structure for a given projected point that is known to correspond to an original structure, then you need to arrange for there to be a mapping from original to projected, and then you can apply the reverse mapping. Very likely, once you've constructed the eigenvectors, the code that is plotting these projected points in 2D space will just take the original structures in order and produce the projected points in the same order. Now the reverse mapping is trivial. If you're after a 3N-dimensional structure for an arbitrary point (x1, x2) in projected space which correspond to eigenectors (v1, v2) in 3N-dimensional space, then you need to construct it from the eigenvectors yourself, as x1*v1 + x2*v2. This structure won't be physically realistic, however. The whole point of the eigendecomposition is that any of the structures used as input can be constructed from a linear combination of the eigenvectors. Hopefully, most of the variation is in the first few eigenvectors so that one can approximate the higher-dimensional space by a linear combination of a few eigenvectors - and the weights in the linear combination are members of a low-dimensional space. If this makes no sense, then reading a few chapters of a linear algebra textbook might be in order. :-) Mark _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
