[gmx-users] pca-based MD

James Starlight jmsstarlight at gmail.com
Mon Sep 24 08:30:06 CEST 2012

I've tried to make PCA from my X-ray data and forced with many problems :)

Firstly I've made pdb trajectory in NMR-like format ( by means of
pymol) consisted of all X-ray structures.

than I've make .tpr file (From the tpr of the same protein which I've
simulated previously) for the subset of C-alpha atoms common to all

Finally I've tried to calculate eigenvectors
Structure or trajectory file has more atoms (2196) than the topology (302)

Does it mean that all structures in trajectory must have only C-alpha
atoms initialy ?

IS there another way to make tpr as well as pdb trajectory files for
such x-ray PCA?


2012/9/24 Thomas Evangelidis <tevang3 at gmail.com>:
> Hi,
> thanks again for explanation. Its also intresting to me is it possible
>> to do further biassed MD guided on that FMA modes as well as obtain
>> projections onto that FMA sub-spaces of X-ray datasets for instance ?
>> ( e.g for comparison of the results from FMA of experimental data as
>> well as MD_data)
>  Have a look at another thread posted today, named "PC comparison between
> two simulations".
> On a second thought, you might want to consider the nudged elastic band
> method and its variants for your case, since you have the initial, the
> final and intermediate states of your protein. Unfortunately they are not
> implemented in GROMACS, but they are in AMBER.
> Thomas
> --
> ======================================================================
> Thomas Evangelidis
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> email: tevang at pharm.uoa.gr
>           tevang3 at gmail.com
> website: https://sites.google.com/site/thomasevangelidishomepage/
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