[gmx-users] Simulated Annealing

Justin Lemkul jalemkul at vt.edu
Mon Feb 4 15:47:51 CET 2019

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 A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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