[gmx-users] Targetted MD in Gromacs?

[Bert de Groot]

David van der Spoel wrote:
> 
> On Fri, 2003-05-23 at 02:58, Jinzhi Tan wrote:
> > Dear Sir:
> > I learn the targetted molecular dynamics in CHARMM. But it is so difficult to me. I wonder Gromacs can do TMD in its future version. Thank you very much.
> >
> can you be more specific?

TMD is a technique originally proposed by Schlitter in which the simulated system
is slowly driven from its initial configuration to a predefined target configuration, 
to study possible transition pathways. AFAIK, it functions such that
that the RMSD to the target structure gradually decreases (or if you like
the radius of the hypersphere around the target structure sampled by the
simulation steadily decreases).

It wouldn't be too difficult to implement in gromacs. In fact most of the
functionality is already present in the ED sampling module.

Bert

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/071/bgroot
____________________________________________________________________________