[gmx-users] PCA two ensembles different atoms order

Nawel Mele nawel.mele at gmail.com
Mon Jul 3 12:09:17 CEST 2017

Hi Peter,

What I have is two REMD trajectories and an NMR ensemble. The two MD
trajectories were not written in the same way in term of atoms order. So I
just rewrite one of them to have the atoms in the pdb files in same order
in term of indices and same for the NMR ensemble so all three ensemble are
the same. For the reference structure I use the first frame of the first
REMD trajectories.

I then did exactly what you said, I calculated the PC for one ensemble and
then then projected the two ensembles and the NMR ensemble onto those PCS
but the results obtained (the PC plots) was looking "weird".
So I decided to looked at my ensembles into VMD and I realised that if I
combined them in one big trajectory the bonds are kind of broken for the
trajectory that I rewrite (because I started the trjconv with the first
ensemble and VMD use the first frame of this ensemble as topology and it
looks like even tough the atoms are in same order vmd is having an issue).
I mean by that that if I open them separately it is fine but combined it is
like vmd does not recognise the atom order. I don't know if it affects the
PCA result.

I don't know if it is clearer?


2017-07-03 10:44 GMT+01:00 Peter Kroon <p.c.kroon at rug.nl>:

> 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.
> Peter
> 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
> >
> >
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Nawel Mele, PhD Research Student

Jonathan W Essex Group, School of Chemistry

University of Southampton,  Highfield

Southampton, SO17 1BJ

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