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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