[gmx-users] Reg:Equilibration

[Justin A. Lemkul]

Anil Mhashal wrote:
> Just plot a graph of the potential energy with respect to the time and 
> check the energy fluctuation, it should be less than 10% of the average 
> potential energy then u can say that ur protein is equilibrated.
> 

I would think that, for most systems, a fluctuation of 10% is quite large.  I 
would expect most stable systems to fluctuate less than 1%, if that.  Even then, 
you can judge very little from potential energy alone.  The simulation may be 
stable at that point, but without more analysis, I'd say it is hard to judge how 
equilibrated the system is.  In my experience, the potential energy generally 
converges within a few ps, but other properties may take substantially longer to 
converge.

-Justin

>  
> 
> On 5 October 2010 17:16, vinothkumar mohanakrishnan <kmvinoth at gmail.com 
> <mailto:kmvinoth at gmail.com>> wrote:
> 
>     hi anil
> 
>     i get the potential energy at the end of the mdrun. if i want to
>     calulate the deviation with what i should compare and calculate the
>     deviation.can you be more specific.
> 
>     Regards
>     Vinoth
> 
> 
>     On Tue, Oct 5, 2010 at 4:51 PM, Anil Mhashal
>     <anil2000.2008 at gmail.com <mailto:anil2000.2008 at gmail.com>> wrote:
> 
>          To check ur equilibration, just look at the potential energy
>         and find out the deviation in the energy if the deviation in the
>         energy is within 10% then ur equilibration is successful...
> 
>         On 5 October 2010 14:56, vinothkumar mohanakrishnan
>         <kmvinoth at gmail.com <mailto:kmvinoth at gmail.com>> 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.
> 
>             Regards
>             Vinoth
> 
>             --
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> 
> 
> 
>         -- 
>         Anil R.Mhashal
>         Research fellow
>         Physical Chemistry Division
>         National Chemical Laboratory
>         Pune 
> 
> 
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> 
> -- 
> Anil R.Mhashal
> Research fellow
> Physical Chemistry Division
> National Chemical Laboratory
> Pune 
> 

-- 
========================================

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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