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

From: Andreas Svrcek-Seiler <>
Date: Tue, 15 May 2007 11:20:16 +0200 (CEST)

> 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.
...When using Langevin Dynamics, you're simulating a canonical ensemble.
For this, some algebra gives a total Energy variance:
Var(E) = k T^2 C_v.
(k...Boltzmann constant, T temperature, C_v heat capacity at constant
Combining that with the equipartition theorem (which gives a heat capacity
of k/2 per degree of freedom under conditions not exactly fulfilled in
MD), this gives
Var(E) ~= k^2 T^2 * (1/2) * 3N (for N atoms).

So you'd expect temperature fuluctuations of about
<E> +- kT * sqrt((3/2)*N).
...With non-harmonic potentials and cutoff this is only a rough estimate
but when I checked (ages ago) the estimate was quite ok for implicit
solvent MD. It should also be obvious that the estimate gives quite huge
numbers for some thousand atoms.

I hope that helps,
good luck

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Received on Wed May 16 2007 - 06:07:27 PDT
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