Re: Minimizing and Equilibrating

From: LEWYN LI (
Date: Mon Jul 17 2006 - 13:52:54 CDT


         From my experience, the number of time steps needed for each stage
depends on a number of things, including the size of your system, how
relaxed/frustrated your initial structures are etc. The "rules of thumb"
I used are:

1. Minimimize until the gradient tolerance drops below 1.0. The number
of steps required to achieve this is system-dependent. I usually just
minimize initially for, say, 10000 steps and periodically check the
gradient tolerance.

2. Equilibrate the fixed protein until the temperature (and other
quantities such as pressure if necessary) stabilizes at the desired value.
Again, the number of steps is worked out by trial and error.

3. Equilibrate with decreasing harmonic constraints until the
unconstrained protein is stable in terms of temperature, structure and
other desired quantities.

         Other people probably have different protocols. Hope this helps!


On Mon, 17 Jul 2006, wrote:

> I am working with a protein solvated in a water box (altogether 450,000atoms). As the tutorial
> suggests, I am going to
> 1)minimize the system
> 2)fix the proteins and equilibrate
> 3) minimize and equilibrate again, with protein free to move.
> I am looking for suggestions regarding the number of timesteps needed for each one of those steps.
> Should there be more equilibration TS's than minimization? If so, are there any suggested relative
> proportions? Should the first and second minimizations/equilibrations have the same number of
> timesteps? How significant is this?
> Thank you very much!
> Anya Yermakova

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