[gmx-users] supervised MD in Gromacs?

[Albert]

Hi:

Here it is:

Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict 
GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale
http://pubs.acs.org/doi/abs/10.1021/ci400766b

In this work, the author captured the ligand binding process in 60 ns.

Here is another one:
Binding pathway of histamine to the hH4R, observed by unconstrained 
molecular dynamics".
http://www.sciencedirect.com/science/article/pii/S0960894X15000645


Briefly: The supervised MD (SuMD) approach exploits a tabu-like 
algorithm to monitor the distance between the center of mass of the 
ligand atoms and the receptor-binding site in short (600 ps) standard MD 
simulations. According to this strategy, an arbitrary number of distance 
points is collected ‘on the flight’ at regular intervals and fitted into 
a linear function f(x)= mx. If the slope (m) is negative, the 
ligand–receptor distance is likely to be shortened and the simulation is 
restarted from the last set of coordinates. Otherwise, the simulation is 
restored from the original set of coordinates and started over. The 
supervision is repeated until the ligand–receptor distance is less than 
5 Å.


I've contacted both authors, but it seems that they are reluctant to 
share any of their methods, protocol or script......

Albert




On 12/08/2015 11:26 AM, João Henriques wrote:
> Dear Albert,
>
> You'll have to provide more information. As it is, I doubt anyone
> understands what you're referring to. What method is it? Where is it
> presented? Etc.
>
> Best regards,
> João