[gmx-users] Targetted MD in Gromacs?

Eric Jakobsson jake at ncsa.uiuc.edu
Sun May 25 19:57:00 CEST 2003

We use another type of restraint, where the structure relaxes towards the 
desired structure by a certain fraction of the distance with each time 
step.  This gives a movement that is essentially completely damped, as 
opposed to a restoring force, which is undamped and gives rise to spurious 
oscillatory modes.

It's pretty straightforward to insert such a restraint as an additional 
option in the module that defines the restraints. (Actually, I didn't do 
this myself--it was done my See-Wing Chiu in our group.)


At 09:55 AM 5/23/2003 +0200, you wrote:
>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
>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
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
405 N. Mathews Avenue
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909

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