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: A Replica Exchange Molecular Dynamics Simulation Study
Still, your post seems to be about simply being unable to unfold at
all. I have unfolded a very stable beta-barrel by either simulating at
3000 K or using the pull code to pull the termini apart. This was not
a real study -- I only used this to make a reverse folding movie for
non-scientists -- but I can verify that it is possible to unfold even
very stable proteins by these methods.
Chris.
-- original message --
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 the other 2ns for 400K
only, then the protein is still stable and the value is almost the
same in radius of gyration.
Below is the mdp file of the heating.
What's wrong with my system?
--
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