[gmx-users] Targetted MD in Gromacs?

Yuguang Mu ygmu at theochem.uni-frankfurt.de
Fri May 23 10:23:00 CEST 2003

Can we define a WEAK distance restrain between two groups of a molecule?
Then so called Targetted MD  can be done in case the targeted structure
is mainly different from the initial one  only in some mobile parts ?

or in case a more or less a rotation have to be performed, can we
define a angle or dihedral restarain, in which cases, the atoms are
not bonded at all ? And this restrain should not effects the exclusion
list .

> 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
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