[gmx-users] all-atom pca

gromacs query gromacsquery at gmail.com
Mon May 11 22:32:21 CEST 2015

Hi All

I am doing PCA and its working fine if I choose few atoms only (heavy) and
I get extreme pdb file having heavy atoms for, say, eigenvector 1. But I
want to have extremes of all-atom structures, so I thought of doing PCA on
all-atoms but I end up with having Segmentation default error which I think
related to comp memory issue.
I think (please correct me) the extreme structures (heavy atoms) would
belong somewhere in the trajectory file. If I can get frame numbers of
these extremes calculated on heavy atoms then I can use same frame numbers
to dump all-atom structures. But how to get frame numbers for these
extremes? may be RMSD with respect to extremes on heavy atoms.


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