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

[Justin A. Lemkul]

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.

-Justin

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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