[gmx-users] Questions Regarding principal components analysis

Catarina A. Carvalheda dos Santos c.a.c.dossantos at dundee.ac.uk
Tue Feb 7 12:04:49 CET 2017


1) Short answer is no. The simplest PCA using GROMACS tools is perhaps
cartesian PCA using g_covar and g_anaeig.

2) Highly depends on the size of your system, its dynamics, and what you
are trying to characterise using PCA.

I recommend you to study this topic a little bit further before performing
this analysis. There are many articles and tutorials on this subject.


On 7 February 2017 at 09:43, Apramita Chand <apramita.chand at gmail.com>

> Dear All,
> I have some questions regarding principal components analysis:
> 1) Is free energy calculations necessary for principal components analysis?
> I have performed usual MD simulations for my system of a small peptide in
> solution. If free energy calculations are necessay , I will have to redo
> all the simulations??
> 2) The simulations are 15-20ns long. Is this sufficient to do PCA?Or is it
> just for longer trajectories?
> Regards,
> Apramita
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Catarina A. Carvalheda

PhD Student
Computational Biology Division
University of Dundee
DD1 5EH, Dundee, Scotland, UK

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