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

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 4 16:08:01 CET 2004

On Wed, 2004-02-04 at 14:44, Anthony Ivetac 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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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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