Dear Hsin-Lin:
I am no expert in this area. I am just saying that if you get
densities that are way too low in NPT, then you might alleviate this
problem with NVT.
In fact, I would personally do this in vacuum without pbc and use the
sd integrator. Then you can sample extended conformations. I'd
consider this a method to generate unfolded conformations that
probably have no relation to the true temperature denatured state. But
let's be honest, you're never going to come close to Boltzmann
sampling of an unfolded state in 300 ns so why bother with the water?
Your link ( http://manual.gromacs.org/online/protunf.html ) is only
concerned with analysis, so it is irrelevant.
If you are determined to use NPT then I suppose that you could use the
Berendsen barostat (more stable in simulations but you get the wrong
ensemble) with a very low compressibility. That's about all I can say,
perhaps somebody else will comment.
Good luck,
Chris.
-- original message --
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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