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

Anthony Ivetac ivetac at biop.ox.ac.uk
Wed Feb 4 14:45:01 CET 2004

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?

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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