[gmx-users] a question related to production MD

[Justin A. Lemkul]

Please keep the discussion on the mailing list.

Acoot Brett wrote:
> Dear Justin,
>  
> My question is a reaction can occur in 2 direction, i.e., forward 
> direction and reverse reaction. As for before the start of production MD 
> the system has fully equilibrated, thus during the whole production MD 
> there will be no significant energy change. But then why the system 
> should converge, or vibrate around the converge conformation, rather 
> than vibrate around the production MD start conformation?
>  

Equilibration is typically done with restraints on the solute.  Thus, the data 
collection stage is the first time that the solute is allowed to move freely. 
Further, equilibration is typically far shorter in terms of time than the actual 
data collection phase.  The timeframe required for the collection of useful data 
varies depending upon the question being asked, but you need to always be 
mindful of the different lengths of time that it takes for various physically 
relevant behaviors to take place.  The extent of change observed between the 
starting an converged structures depends entirely upon the inherent behavior of 
the molecule(s) being studied.

-Justin

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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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