Hey,
NPT is not the appropriate way to do this kind of simulations. I am not sure
whether or not the water models available for classic MD simulations are able
to reproduce the phase behavior. Indeed what you see when your system explodes
and gets huge is the water evaporating. What is gene
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 conformatio
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.
Dear Hsin-Lin:
The first thing that comes to mind is using very high temperatures with NVT.
Obtaining the desired denatured state is a complex challenge, but you
might try this paper:
Phys. Rev. Lett. 93, 238105 (2004)
Reversible Temperature and Pressure Denaturation of a Protein
Fragment:
Hi,
I have question about unfolding.
I use three different ways respectively but all failed.
The three way is,
1. 600K in 20ns, then the system explode.
2. 400K in 10ns, the protein is very stable and the value is almost the same in
radius of gyration.
3. heating up from 300K to 400K in 2ns and
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