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

Justin A. Lemkul jalemkul at vt.edu
Tue May 31 02:03:51 CEST 2011

bharat gupta wrote:
> Well, mine is a beta-barrel protein called Green Fluorescent Protein. In 
> such a case the movement of ion is very important. As the ion in side 
> the barrel can quench the fluorescence. That's what I want to track.. 

You can probably address this with the methods I've described.  That's likely 
all that anyone can offer.  Spend some time looking through the literature at 
the many kinds of systems that have been addressed using SMD and/or umbrella 
sampling and come up with a coherent plan to address your system based on what 
you find.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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