[gmx-users] Fluctuation dissipation

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 15 14:10:22 CET 2006

Paolo Cerri wrote:
> 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?
This is very dependent on the reliability of your fluctuations. Do you 
use reliable coupling algorithms (i.e. not Berendsen)?

> Paolo 
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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