[gmx-users] Principal Components Analysis in Gromacs

[Tsjerk Wassenaar]

Hi James,

> 1- I want to increase amplitude of the motions seen on the selected PCs but
> I can't found scalling factor option for that.

The analysis gives you the amplitudes that are in your trajectory. Why
do you want to amplify them to something probably non-physical?

>
> 2- I have calculated MD trajectory for my protein. From this trajectory I
> want to find some relevant motions by means of PCA analysis. Also I have
> dataset of the experimental structures of that protein where this motion
> also presents ( e.g active and innactive conformations of my protein
> included in my dataset) As the consequence I want to compare overal
> direction of the motion observed along some PCs calculated from MD
> trajectory ( it's called EDA) with the motion observed olong other PCs wich
> was calculated from the enssemble of the pdb structures. As I've noticed
> via  g_anaeig I can compare such datasets by means of -v and -v2 flaggs. For
> this purpose I must make trajectory for my X-ray structures at first and
> load it with the MD trajectory into the g_anaeig -v md.trr -v2 x_ray.trr.
> Would this aproach be correct in general ? What should I do if both of my
> datasets consist of different number of backbone atoms (due to some missing
> residues in the X-ray data) ?

You have to make sure that the trajectories and the eigenvectors
match. Then you have to think of what you want to do.

- If you want to project the x-ray structures onto the eigenvectors
from the MD simulations, you have to use

g_anaeig -v eigenvec_from_md.trr -s reference.tpr -f xray_structures.pdb -proj

- If you want to compare the similarity of the eigenvectors obtained
from MD and from your crystal structures, you have to do PCA on both
sets separately and then

g_anaeig -v eigenvec_from_md.trr -v2 eigenvec_from_xray.trr -eig
eigenval_from_md.xvg -eig2 eigenval_from_xray.xvg -s reference.tpr
-inpr

Cheers,

Tsjerk

>
>
> Thanks for help,
>
>
> James
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands