Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"

From: David A Case <>
Date: Mon, 11 Nov 2013 09:18:23 -0500

On Mon, Nov 11, 2013, 冉挺 wrote:

> I did another 4 * 100 ps simulation. I sampled snapshots every 100 steps
> (100 fs). The RMS fluctuation was narrowed a lot and kept stable at the
> last 3 * 100 ps, but the average DV/DL value changed. So which
> average DV/DL value of the four simulations should I used for integration.

As with other properties, the value you want for <DV/DL> is the equilibrium
average. This means that you generally must discard values obtained during
the "equilibration" phase, and only use those once the system has become
stable. Depending on you system, 400 ps might or might not be long enough to
establish a good equilibrium; (it probably is too short a time except for very
simple systems.)


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Received on Mon Nov 11 2013 - 06:30:02 PST
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