[gmx-users] supervised MD in Gromacs?
mailmd2011 at gmail.com
Tue Dec 8 11:33:03 CET 2015
Here it is:
Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict
GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale
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
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
I've contacted both authors, but it seems that they are reluctant to
share any of their methods, protocol or script......
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,
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