[gmx-users] Fluctuation dissipation

Berk Hess gmx3 at hotmail.com
Wed Feb 15 14:10:51 CET 2006

>From: Paolo Cerri <Paolo.Cerri at mi.infn.it>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] Fluctuation dissipation
>Date: 15 Feb 2006 12:39:47 +0100
>Dear Gromacs users,
>I'm running md simulation of hydrophobic aminoacids in water. I evaluate
>the heat capacitance for the system at constant volume by computing the
>derivative of the energy with respect to temperature (for which the
>ratio Delta E / Delta T provides an estimate if Delta T is small enough)
>at T=300
>I expect the following relation to hold
><E^2> -<E>^2 |at T=300 == K* T^2 *(Delta E/Delta T)
>as stated in the fluctuation dissipation theorem
>However I obtain values for the right side of the above equation that
>are nearly 4 time larger that the left side.
>Has anybody experienced the same problem?

Might it be that you have used the Berendsen thermostat for
pressure coupling?
In that case the energy fluctuations are incorrect.


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