[gmx-users] simulated annealing

[Justin A. Lemkul]

leila karami wrote:
> Dear Justin
> thanks for your attention
>  
> I want to use simulated annealing to obtain global minimum for 
> protein-dna structure. I will do first heating and then slowly cooling.
>  
> is my mdp file true, now?
>   
> T-couple = brendsen
>  
> ref-t = 300
> 
> annealing: single
> 
> annealing_npoints: 5
>  
> annealing_time: 0  3  6  9  12 
>  
> annealing_temp: 150  650  600  550  500  450  400  350  300
> 

No.  Using ':' to separate lines will cause grompp to not read the parameters. 
Use '=' to separate parameters and values.  Further, the parameter 'T-couple' 
does not exist, it is tcoupl.  Also note that 'Berendsen' is spelled 
incorrectly, which will also cause grompp to give an error about an unrecognized 
parameter.

I'm also assuming (based on having only a single value of annealing_npoints) 
that you are coupling the entire system to one thermostat.  Doing so is 
unreliable, and the consequences have been discussed numerous times across the 
list and in the references provided on the Gromacs wiki:

http://www.gromacs.org/Documentation/Terminology/Thermostats

Further, you give 9 values of annealing_temp, but based on annealing_npoints, 
you should have 5 (if you only have this single group).  Please refer to the 
manual.  An example of proper usage is even provided online:

http://manual.gromacs.org/current/online/mdp_opt.html#sa

-Justin

> Best regards.
> 

-- 
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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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