[gmx-users] essential dynamics

[Bert de Groot]

Euston, Stephen R wrote:
> Hi,
> 
>  
> 
> I am hoping to use essential dynamics to look at unfolding of proteins
> (probably barley lipid transfer protein and bovine beta-lactoglobulin).
> I have searched the Gromacs database, and the web but I can find very
> little info on the actual process of running the simulation. I have also
> looked at the WHAT IF home page, and again I can’t seem to find much
> here either. Does anyone know of a web tutorial or other that covers
> essential dynamics simulations?
> 
>  
> 

make_edi -h gives some coarse info with a number of references.

there are also still a number of slides online that sketch the way the different
constraint algorithms work:

http://www.mpibpc.gwdg.de/groups/de_groot/presentations/edsam/

for protein unfolding you may also consider conformational flooding, which is
implemented in gromacs as well: again make_edi -h or
http://www3.interscience.wiley.com/cgi-bin/abstract/112750179/ABSTRACT

cheers,

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
http://www.mpibpc.mpg.de/groups/de_groot