[gmx-users] stay at some temperature during annealing

[Justin Lemkul]

On 6/11/13 1:11 AM, mu xiaojia wrote:
> Hi guys,
>
> I am using simulated annealing for my protein+water+Ion system, I tried to
> let the system stay at some temperature for a while, e.g.: stay at 600k
> from 3000ps to 10000 ps, then gradually cool it down to 298k, so my mdp is
> like:
>
> annealing_time = 0 3000 10000 20000 0 3000 10000 20000 0 3000 10000 20000
> annealing_temp = 298 600 600 298 298 600 600 298  298 600 600 298
>
>
> however, error message is:
>
> Found 12 annealing_time values, wanter 9
>
> apparently, the "600 600" does not work, does anyone have any suggestion,
> or I could only separate the simulation? Thanks very much!
>

The approach should work, but is also dependent upon other settings.  Can you 
please provide a full .mdp file?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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