[gmx-users] Reg:Equilibration

[Justin A. Lemkul]

vinothkumar mohanakrishnan wrote:
> Hi all
> 
> Suppose say i have a box of decane molecules and i want to equilibrate. 
> say i have all the necessary files to run mdrun. on what basis i say 
> whether my equilibration is successful r not after the mdrun. what 
> properties i should measure to know whether my equilibration was successful.
> 

Beyond making sure your ensemble has converged (i.e. temperature and/or 
pressure), I would suggest you do some homework and find out how others judge 
such systems to be stable and reliable.  What do they measure, and why do they 
do it?  Such an exercise is of greater benefit to you than someone spoon-feeding 
you some instructions (for which there may not be a generalized answer).

-Justin

> Regards
> Vinoth
> 

-- 
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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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