[gmx-users] meaning of minus potential and buried surface area

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 22 00:31:54 CEST 2011

ahmet yıldırım wrote:
> Dear users,
> 1.) During the simulation the mean potential energy is minus (-) value. 
> What does this mean? Why minus?

Net attraction.

> 2.) let's say, Interface/Buried Surace Area (ISA) between protein and 
> ligand was calculated and hydrophobic ISA obtained greater than 
> hydrophilic ISA. What does this mean?

That, as you might expect, hydrophobic groups are shielded from the solvent to a 
greater extent than polar groups.


> No one is my special advisor but If you help me, I will be happy.
> Thanks in advance
> -- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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