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

Anthony Ivetac ivetac at biop.ox.ac.uk
Mon Feb 9 11:26:01 CET 2004

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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