[gmx-users] Re: simulation of protein/water and phosphate ion

[Justin A. Lemkul]

bharat gupta wrote:
> HI,
> 
> I have tried simulating my protein (GFP) solvated with water molecules 
> and 10 phosphate ions. During the md run step the system starts 
> exploding after  500 ps. What could be the reason for this . I know this 
> is happening due to the addition of phosphate ion but I need to study 
> the binding of ions . So, what shall I do ??
> 

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-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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