[gmx-users] ED sampling and overall rotation

Bert de Groot bgroot at gwdg.de
Fri May 13 17:11:46 CEST 2005

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,


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

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