[gmx-users] The reproduction of Barnase-Barstar binding energy

[Paris Tzou]

Dear all,

    I am trying to reproduce the Barnase-Barstar binding energy  published
in 2010 in Biopolymers entitled "Downhill Binding Energy Surface of the
Barnase–Barstar Complex"   by using Umbrella sampling introduced in the
Gromacs tutorial page
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html


    I follow the parameter setup found in the paper but the binding energy
is around 210 KJoul instead of 40 KJoul. That's a big difference. Since the
affinity constant of Barnase-Barstar is known, this test of reproduction is
important in proving Umbrella Sampling can be used to estimate the binding
energy.

    Does anybody have any suggestion ?

Thanks a lot for your time,

Paris

 @@@@@@@@@@@@@@@@@@@@@@@@
  Paris Tzou
  Department of Bioscience and Biotechnology
  National Taiwan Ocean University
  2, Pei-Ning Road, Keelung, Taiwan 20224, R. O. C.
  Office: 886-2-2462 2192 ext  5522
  Fax: 886-2-2462 2320
  Cellular: 0928 305 905
  E-mail: paristzou at gmail.com