[gmx-users] Fwd: PCA two ensembles different atoms order

Peter Kroon p.c.kroon at rug.nl
Mon Jul 3 13:40:44 CEST 2017

Hi Nawel,

I'll admit that I'm out of my depth PCA-wise from here on out, so I
heartily invite the rest of the list to chip in.

Could it be that there's simply poor correlation between your
simulations and your NMR ensemble?


On 03-07-17 12:34, Nawel Mele wrote:
> 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?
> Nawel
> 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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