On Thu, 2014-03-27 at 20:33 +0530, Gargi Borgohai wrote:
> 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.
This force field is ~20 years old with well-known and well-documented
deficiencies. There is no reason to continue using it (it was a great
contribution at the time and served as an excellent foundation for later
efforts, but ff94 is a horrible choice today).
> 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?
No. Use a better force field. There's a chapter in the Amber manual
regarding force fields. The currently recommended choice is ff12SB.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 27 2014 - 08:30:03 PDT
