Re: AMBER: Energy Spread using GB & Langevin Dynamics (NAB)

From: David A. Case <>
Date: Mon, 14 May 2007 14:40:50 -0700

On Mon, May 14, 2007, wrote:

> Hi, I've run some MD simulations (simulated annealing from 500 --> 400
> --> 300 with 100,000 steps per temperature), and realised that in my
> MD run, the energy and temperature fluctuations are rather large.
> (Total energy as
> given in the "MD:" row). Energy fluctuations are ~80kcal/mol, while
> temperature fluctuations are ~50K.
> Are these values to be expected? They seem far larger than what I
> would think MD should give.
> Here are my MD options:
> (1396 atoms, 1141 frozen)

If you really have only 45 moving atoms, you should expect very large
temperature fluctuations. This has been discussed earlier on the mailing

...hope this helps...dac

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Received on Wed May 16 2007 - 06:07:21 PDT
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