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.
--
========================================
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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