On 21/04/2010 10:19 PM, leila karami wrote:
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?
Try it and see. Note that a single annealing procedure is not guaranteed
to find the global minimum - no non-exhaustive algorithm can. I'm
struggling to see why being there would matter for a starting structure
for MD.
Tcouple = berendsen
That still won't work, as Justin told you.
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?
If you'd done your homework and read some literature where other people
had done such annealing processes, you'd have a good idea whether this
is true.
2) is there relation between (annealing_time = 0 3 6 9 12 15 18
21 24) and (dt and nsteps)?
Yes. 7.3.16 of the manual clearly shows what that is.
Mark
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