bbgm - the discussion - Latest Comments in Your Monday evening simulations

Re: Your Monday evening simulations

Emad Tajkhorshid — Tue, 01 Jul 2008 18:36:28 -0000

Right. We cannot be too technical for the news release. I am happy the explanation was acceptable. We seem to be now able to take MD of large biomolecular systems to the next level of time scale, which allows us to observe more biologically relevant events. For this work we have multiple 100-ns long simulations, which allowed us to capture the entire process.

I look forward to more exciting results too.
Take care,
Emad

Re: Your Monday evening simulations

mndoci — Tue, 01 Jul 2008 08:52:25 -0000

and happy to see that people in the MD community are reading blogs

Re: Your Monday evening simulations

mndoci — Tue, 01 Jul 2008 08:51:45 -0000

Emad, that makes more sense. Something got lost in translation going from what you just said to the press release language (and my rather tired brain)which made it sound like the first ever ligand binding simulation :).

It is a really cool simulation, and as you point out, no biasing potential. Looking forward to more

Re: Your Monday evening simulations

Emad Tajkhorshid — Tue, 01 Jul 2008 07:10:04 -0000

Hi Deepak,

Thanks for posting this. The simulation of ADP binding to a carrier is indeed the first simulation of its kind, as it simulates the entire binding of a ligand over a distance of more than 20A to its binding pocket, (and here is the key word:) under fully equilibrium conditions, i.e., WITHOUT applying a force or a biassing potential, or even putting the ligand very close to its binding site. As far as I know there is no other report of this kind in the literature. Correct me if I am wrong.