[gmx-users] Re:Energy landscapes

[lloyd riggs]

Dear All,

I remember a post in the last couple months but cant find it.  In any case, by searching through van der groot et alls. papers, the -xmin, -xmax, -dim and -ngrid options third point, example: -xmin 3 3 3 -xmax 3 3 3 is for reading in the output 3d (projections on V1, V2, V3 or first three vectors, and is output as xyz points in a pdb file.  This can be read into various ploting or even pymol/vmd to illustrate the projection on a PCA of 3 dimensions.  From the lit it is supposed to show 2 or more conformational states, and a number of intermediary states in between (overall just a 3d PCA graph).  If I am wrong please correct me, but this is what the output for me was doing, and I personally prefer the 2D, as its easier to illustrait (as images in 3d lack the necessary rotation to show everything in a static image).

Sincerely,

Stephan Watkins