[gmx-users] Targetted MD in Gromacs?

David van der Spoel spoel at xray.bmc.uu.se
Fri May 23 09:30:01 CEST 2003

On Fri, 2003-05-23 at 09:15, Bert de Groot wrote:
> 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.
A possibility is to just use weak position restraints, but that may not
be enough. The ED technique just forces movement along the first three
eigenvectors, doesn't it? Another possibility is to use g_morph or
g_dyndom to create structures along a reaction coordinate and simulate
these to get a continuous path.

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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