[gmx-users] simulated annealing

[leila karami]

Dear Justin
thanks for your accuracy.
I want to use simulated annealing to obtain global minimum for
protein-dna structure. I will do first heating and then slowly cooling and I
will my full md simulation in 300K. is my manner true?
if so, is my mdp file true, now?

Tcouple = berendsen
ref_t = 300
annealing = single
annealing_npoints = 9
annealing_time = 0  3  6  9  12 15  18  21  24
annealing_temp = 150  650  600  550  500  450  400  350  300

my main questions are that
1) is last line of mdp file suitable for simulated annealing?
2) is there relation between (annealing_time = 0  3  6  9  12 15  18  21
24) and (dt and nsteps)?
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