[gmx-users] Fwd: Simulation of protein with phosphate ion...

[Justin A. Lemkul]

bharat gupta wrote:
> Thanks a lot.. If I am not wrong SMD and Umbrella sampling will help me 
> in determining the binding affinity. So, my first objective can be 
> achieved with it.
> 
> Then what about the movement of ions into the barrel. Will it be 
> possible to track it with MD coz the movement of ion is very important 
> in my case. I don't want them to enter the barrel rather I want them to 
> be on the surface of the barrel??
> 

You can implement such restraints, or guide the ion through the channel, 
whichever you prefer.  The literature is rich with studies of the movement of 
ions and small molecules through transporters and channels.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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