[gmx-users] potential energy value

[Justin A. Lemkul]

ahmet yıldırım wrote:
> Dear users,
> 
> I tried the emol values the following:
> 
> As emol=2000, Potential energy=-4.7x10^5
> As emol=1000, Potential energy=-4.9x10^5
> As emol=100, Potential energy=-5.2x10^5
> 
> Generally, when we did the energy minimization:
> 
> how much potential energy value=?  we can say that the energy 
> minimization is good.
> 

Potential energy depends on the content of the system, as well as the extent of 
minimization.  The purpose of EM is to generate a reasonable starting structure 
for MD such that the forces do not cause it to explode when you start your 
simulation.  There is no magical cutoff that determines if you're done; you have 
to apply some of the underlying theory to your system and judge that yourself.

-Justin

> 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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