|
|||||||||||||||||||||||||||||||||
AMBER Archive (2006)Subject: AMBER: Replica exchange rate in REMD
From: Seongeun Yang (seongeun_at_korea.ac.kr)
Hello all,
I have some general questions in running replica exchange and conventional MD simulations.
1. Do the replicas always have to be exchanged after their potential energies are relaxed enough to equilibrium?
2. If the total potential energy relaxes quite slowly due to a big system size (e.g. a polypeptide+solvent molecules),
This is what I found in some papers cited quite frequently.
3. If the nonbonding cutoff is set to be 8.0 angstrom in md imput,
4. If the solute polypeptide can be unfolded during simulations,
I'm wondering the answer to the last question is really 'yes' to so many simulation studies reported in the literature.
If the answer is 'no', what is the 'secret' in using a seemingly very small simulation boxes?
Thanks for your reply in advance.
Seongeun Yang
| |||||||||||||||||||||||||||||||||
|