Dear AMBER Users,
I wanted to carry out an REMD simulation of a 20-residue mini-protein in 6M
urea solution. I have used amberff94 force field. As reported in
literature, the native state should retain 60% of folded state (in 6M urea
solution) at 280K with REMD simulation. In my study the results matches
till 20ns of simulation. But beyond 20ns the folded fraction of the peptide
abruptly decreased to 33%.
Should I stop the simulation at 20 ns and start analysing the results?
Looking forward for your kind advice.
Yours sincerely
Gargi Borgohain
PhD Scholar
IIT Guwahati
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Received on Thu Mar 27 2014 - 08:30:03 PDT
