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

[Justin A. Lemkul]

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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     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>
> 
>     ==============================__==========
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/__mailman/listinfo/gmx-users
>     <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>     Please search the archive at
>     http://www.gromacs.org/__Support/Mailing_Lists/Search
>     <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>     <http://www.gromacs.org/Support/Mailing_Lists>
> 
> 
> 
> 
> -- 
> 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

========================================