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.
-Justin
Any help will highly appreciated!
--
========================================
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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