[gmx-users] simulated annealing (SA)

Justin A. Lemkul jalemkul at vt.edu
Wed Apr 28 13:26:51 CEST 2010

shahab shariati wrote:
> Hi gromacs users
> about SA simulation, I saw in some papers that annealing _time is very 
> short. fpr example [The temperature was increased from 0 to 600 K over 
> the first 4 ps, held at 600 K for 2 ps, and then slowly cooled to 0 K 
> over 14 ps in simulation of protein-dna]. Is there limitation in 
> election of annealing _time? what is optimum value for annealing _time?

The time necessary will depend on the size of the system and the degree to which 
temperature affects it.  You may have to play around a bit to determine what is 
reasonable for your system, and if whatever you're doing accomplishes whatever 
goal you have for the SA procedure.


>  Any help will highly appreciated!


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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