ahmet yıldırım wrote:
Dear Justin,
If possible, can you some explain "net attraction"?
Forces are either attractive or repulsive. "Net attraction" means attractive
forces dominate over repulsive ones. Please consult some elementary physics or
chemistry textbooks for more on these concepts and how they might apply to MD
simulations.
-Justin
Best regards
2011/9/22 Justin A. Lemkul <[email protected] <mailto:[email protected]>>
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
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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Ahmet YILDIRIM
--
========================================
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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