[gmx-users] Can't unfold the protein

[Hsin-Lin Chiang]

Dear Chris,

Thank you for your reply. 
My protein is very stable.

I simulated it in 300ns in 300K before but there was almost no change. 
That's why I want to do denaturation now.

I want to start a new simulation on the protein which is unfolded. 
And I'll read the paper you told me. 
Thank you.

But I don't understand what you recommend me to do. 
You use 3000K on your protein and the protein unfolded. 
I use 600K on my protein but the system explode(box become very big and protein locate at corner).

I saw the second way on this web, 
http://manual.gromacs.org/online/protunf.html 
But it also useless to me.

And in my mdp I use thermostat and barostat, which means my system is NPT. 
Does anything wrong in my methods?

Sincerely yours,

Hsin-Lin 
 
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