[gmx-users] pca-based MD

Thomas Evangelidis tevang3 at gmail.com
Sun Dec 16 12:19:32 CET 2012

Hello James,

I'd like to ask you some addition questions about FMA. As I understood
> from the FMA page that technique is something like integrator of
> principal components (merge some PCs with identical functional motion
> seen in the X-ray structures for instance) calculated from g_covar. So
> FMA is also Hessia-based method (assuming that cov.matrix is inverse
> of the Hessian) for studing functional motion in protein isnt?

FMA follows PCA, so this is correct.

> Some technical questions:
> Have you tried to extract functional modes from X-ray data set (not
> from of unbiased md as in case of EDS) of your kinase for further
> md-guiding ( e.g by means of EDS) of that protein along some
> functional modes?
> Have you tried use it with the gromacs 4.5 ? I've found that only for
> older gromacs releases.
> Does it possible to visualise motion along FM in vmd or mol script ?

I haven't tried that for the simple reason that one needs multiple X-ray
structures resembling different stages of the thermodynamic cycle to draw
solid conclusions about functional modes. In my case there were not many
structures available. But if there are many structures for your protein
then you could make some very nice conclusions about the functionally
relevant motions which will also have experimental validity (it will be
easier to convince the reviewer that what you describe is not artificial).
Just be cautious to select the structures that are relevant to the
phenomenon you study (presence of crystal contacts, inhibitors, cofactors,

You don't need to worry about the GROMACS version, the only reason you need
GMX 3.3 is to compile fma and g_anaeig2, the rest of the GMX Tools can be
of any version.

g_anaeig2 can create two types of multi-model .pdb files for visualization,
the maximally correlated motion (MCM) and the ensemble-weighted maximally
correlated motion (ewMCM). I prefer making videos using the latter with
UCSF Chimera, but this is your choice.




Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/

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