[gmx-users] ED sampling and overall rotation

[Bert de Groot]

Thomas Stockner wrote:
> Hi Bert,
> 
> thanks for your answer. One more thing is unclear.
> 
> The eigenvectors used for enhanced sampling define directions in space. 
> During a simulation, my protein will move and tumble and the initial 
> orientation will not match with the orientation at a later time point of 
> the simulations.
> How is this overall rotation of my molecule taken into account when 
> projecting the MD step onto the subspace spanned by the eigenvectors 
> that are used for enhances sampling?
> 

When edsam is activated, the structure is fitted every step to a reference
structure, projected, corrected (if necessary) and translated/rotated back.

That way, the edsam corrections only affect the internal degrees of
freedom, without perturbing the overall motion of the protein (diffusion,
tumbling).


Bert

________________________________________________
Bert de Groot, PhD

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de
http://www.mpibpc.mpg.de/groups/de_groot