AMBER Archive (2005)

Subject: Re: AMBER: langevin, GB and simulated annealing - 3

From: David Case (case_at_scripps.edu)
Date: Tue Apr 26 2005 - 09:06:08 CDT

On Tue, Apr 26, 2005, pascal.baillod_at_epfl.ch wrote:

> To use Langevin dynamics, you could set a series of target temperatures,
> (say 600, 500, 400, 300, 200, 100, 10, etc.) to take effect at different times
> during the simulation. This could have the effect of fairly slow cooling.
> But the Berendsen approach seems to me to be a more natural way of carrying
> out simulated annealing.
>
> Practically speaking, you mean there would be one simulation for each of
> these temperatures, so that in the end I would have to paste the trajectory
> and energy files? Or are there any tools to do that in one single simulation
> in amber?

You can easily set the target temperature to be different at different times
during the simulation. In fact, the input file you posted does this:

> &wt
> TYPE='TEMP0', istep1=0, istep2=400000, value1=0.0, value2=300.0,
> &end
> &wt
> TYPE='TEMP0', istep1=400001, istep2=32000000, value1=300.0, value2=300.0,
> &end

...dac
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