[gmx-users] Re: starting temperature equilibration phase

[Justin Lemkul]

On 8/6/13 2:45 PM, ypca wrote:
> Thank you for the help!
> I can completely understand you, but what about the simulated annealing,
> isn't it automatically for all systems?

No.  If you want to perform simulated annealing, use simulated annealing options 
(see the manual).

> Why the increase of temperature is so fast, like in lysozyme tutorial
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/06_equil.html)?
>

It's not an increase, per se.  The approach used there (which is quite common) 
is to simply assign random velocities according to a Maxwell distribution at the 
desired temperature.  There is not discrete heating phase.

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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