[gmx-users] simulated annealing
Mark.Abraham at anu.edu.au
Wed Apr 21 15:22:56 CEST 2010
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
> 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
> 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.
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