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
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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: parist...@gmail.com
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