[gmx-users] Simulated Annealing

[Shan Jayasinghe]

Dear Prof. Justin,

Thank you very much for the answer. It is really helpful.

On Tue, Feb 5, 2019 at 1:48 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/1/19 4:45 PM, Shan Jayasinghe wrote:
> > Dear Gromacs Users,
> >
> > I did a simulated annealing for my system and now I want to analyse my
> > data. Can anyone suggest me a tutorial for this? What type of information
> > we can get from simulated annealing?
>
> Usually annealing is just applied during equilibration to slowly change
> the temperature of the system. Whether or not it's actually beneficial
> is debatable. The temperature changes so quickly that you don't actually
> sample any sort of thermodynamic equilibrium at any given temperature,
> so there's no really useful analysis that I can think of.
>
> > I want to know whether the generated .gro file corresponds to the last
> > temperature we defined in mdp file?
>
> The final coordinate file written by mdrun always corresponds to the
> final frame, regardless of input settings. It may or may not correspond
> to a state at exactly the temperature specified in the .mdp file.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
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>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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-- 
Best Regards
Shan Jayasinghe