[gmx-users] pca-based MD

James Starlight jmsstarlight at gmail.com
Mon Sep 24 13:52:39 CEST 2012

I've still made such 'only c-alpha ensemble' of my structures by the
other software and performed x-ray PCA. As the result I've extracted
eigenvectors and obtained reasonable distribution (projection) of the
structures along that eigenvectors.

Now I have questions about pca-biassed MD_run. I've made *.edi file
from eigenvectors calculated based on the c-alpha atoms of my x-ray
ensemble. How I could use it with my system consisted of much more
atoms (full atomic protein + solvent) than smaller c-alpha subset of
the x-ray data (only c-alpha atoms from the same protein) ?
i.e if I run mdrun -v -deffnm MD -ei sam.edi

I obtain error about mismatching of atom number from the edi as well
as system.tpr .
Is there any way to extrapolate number of atoms in the sam.edi ?


2012/9/23, James Starlight <jmsstarlight at gmail.com>:
> 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
> structures
> 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?
> James
> 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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