[gmx-users] all-atom pca

Tsjerk Wassenaar tsjerkw at gmail.com
Mon May 11 22:47:04 CEST 2015

Hi Jio,

The scores for all-atom structures will be strongly correlated to those for
heavy-atom structures. So you can use the times for the heavy-atom extreme
projections to extract all-atom structures.



On Mon, May 11, 2015 at 10:32 PM, gromacs query <gromacsquery at gmail.com>

> 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.
> Thanks
> Jio
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Tsjerk A. Wassenaar, Ph.D.

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