[gmx-users] PCA two ensembles different atoms order

Peter Kroon p.c.kroon at rug.nl
Mon Jul 3 11:44:56 CEST 2017

Hi Nawel,

I'm not quite sure what you're trying to achieve, or how, or what
exactly is "wrong".

In general though: calculate the principle components only once, for one
of the ensembles, and project both ensembles on those PCs to get
comparable results.


On 03-07-17 11:37, Nawel Mele wrote:
> Hi all ,
> When performing a PCA of two different ensembles of the same molecule the
> atoms of each molecule need to be in the same order ( same atom name
> associated to the same index) right ?
> However, my two ensembles, even being the same molecule ( different
> starting confirmation ), had their atoms in different order . So I simply
> build a python script to rewrite the ensemble in a same way . Everything
> went right but once I performed the PCA I obtain " wrong " result . Looking
> at both ensembles separately in vmd they are fine , the rewrite ensemble is
> not broken but if I combined the ensemble they don't " like each other "
> like if they weren't the same molecule so don't have the same topology ,
> I don't know if it clear .
> Does anyone had to deal with that ?
> Regards,
> Nawel

More information about the gromacs.org_gmx-users mailing list