[gmx-users] PCA two ensembles different atoms order

Nawel Mele nawel.mele at gmail.com
Sat Jul 1 07:14:49 CEST 2017

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 ?



Nawel Mele, PhD Research Student

Jonathan W Essex Group, School of Chemistry

University of Southampton,  Highfield

Southampton, SO17 1BJ

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