[gmx-users] Targetted MD in Gromacs?

[Bert de Groot]

David van der Spoel wrote:
> 

> A possibility is to just use weak position restraints, but that may not
> be enough. 

right. especially since restraints will produce strong forces when far
from the target and weaker ones when approaching it, which might produce
serious artefacts on the obtained path.

> The ED technique just forces movement along the first three
> eigenvectors, doesn't it?

no. It can, but it can also impose other kinds of constraints, among
which the systematic approach towards a target structure. And not only along
the first three eigenvectors, but along an arbitrarily large subset.
(possibly if one takes the full set of all-atom eigenvectors, this might
formally be the same as TMD, but this would be overkill practically; for
TMD one doesn't need the detour via collective coordinates).

> 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.
> 

yes but then you already predefine the path and the simulated path derived
from that will not be far from the interpolated one, whereas the true path(s)
might deviate significantly. In TMD (or ED sampling with a target) only
the target itself is predefined, not the path. So the system will choose
the (or a) low energy path that may be very different from the interpolated
path between initial and target structure (with the only constraint that
no configuration on the path is farther from the target than the initial
configuration).

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
____________________________________________________________________________