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

[Kay Gottschalk]

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