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From: Andreas Svrcek-Seiler <svrci.tbi.univie.ac.at>

Date: Tue, 15 May 2007 11:20:16 +0200 (CEST)

Hi,

*> 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

volume)

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

Andreas

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

Date: Tue, 15 May 2007 11:20:16 +0200 (CEST)

Hi,

...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

volume)

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

Andreas

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

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