[gmx-users] Directed MD - Transition Paths in GMX

[Ran Friedman]

I think that "steered MD" is something like the pull option in Gromacs,
therefore I doubt if that's the right approach here...

Ran.

Kay Gottschalk wrote:

> Can't you use NOE-like restraints with increasing force constants to
> drive the system where you want it? There are quite a few papers by
> Schulten and Karplus about 'steered MD', I think. I don't know how they
> implemented it, though.
> K.
>
> On Feb 9, 2004, at 12:25 PM, Anthony Ivetac wrote:
>
> > Thanks David. However, rather than interpolating the intermediates
> > between 2 end-point structures, I am trying to get to the 'open' state
> > from the 'closed' state through MD, because I am interested in seeing
> > the impact of this 'opening' motion on an adjacent subunit.
> >
> > I have no experience of playing with the Gromacs code - does anyone
> > know
> > how easy it would be to modify the potential energy function to include
> > some distance contraints? For example, for every step, I would want to
> > calculate the RMSD between the current structure in the simulation and
> > the 'end-point' structure -> RMSDs closer to the end-point would be
> > encouraged and RMSDs away from the end-point would be penalised.
> >
> > Many thanks!
> >
> >
> > David van der Spoel wrote:
> >
> >>> I'm wondering if anyone has implemented a modified version of Gromacs
> >>> which will handle the directed simulation of a protein moving from
> >>> one
> >>> conformation to another?
> >>
> >> **********************************************************************
> >> **
> >> Not really, but you can use the g_morph or g_dyndom program to
> >> generate
> >> a trajectory connecting two structures. Then you can take these
> >> structures and minimize them. The latter program assumes that you have
> >> used the dyndom program beforehand (which is not part of gromacs, but
> >> is
> >> in CCP4.)
> > >**********************************************************************
> > *
> >>
> >>> For example, given 2 crystal structures of a protein in an 'open' and
> >>> 'closed' state - we would start from the closed state and direct the
> >>> protein towards the open state. This could be done by measuring the
> >>> RMSD
> >>> between the simulated structure and the 'target' structure at each
> >>> step
> >>> - encouraging progressively smaller RMSD values until the simulated
> >>> structure superimposes with the target structure (using some sort of
> >>> penalty function).
> >>>
> >>> This is basically the strategy used by Guilbert et al. in their Path
> >>> Exploration with Distance Constraints (PEDC) method.
> >>>
> >>> If anyone knows of any other techniques to direct a protein from one
> >>> conformation to another, with GMX, please let me know!
> >>>
> >>> Many thanks.
> >>>
> >
> >
> > _______________________________________________
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> >
> Dr. Kay-E. Gottschalk
> Department of Biological Chemistry
> Weizmann Institute of Science
> Rehovot
> Israel
>
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--
------------------------------------------------------
Ran Friedman
Laser laboratory for fast reactions in biology
Department of biochemistry
Faculty of life sciences
Tel-Aviv university
972-3-6409824
------------------------------------------------------


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