[gmx-users] Bug in g_energy for calculating heat capacity?

David van der Spoel spoel at xray.bmc.uu.se
Sun Dec 21 10:28:19 CET 2008

Zhang Zhigang wrote:
> Hi, all,
>      Actually I think others have also noticed this "bug": g_energy 
> often generate incorrect heat capacity.  When I checked the source code 
> of gmx_energy.c, I found the calculation of heat capacity is only 
> related with the fluctuation of temperature, which is actually the 
> algorithm for NVE ensemble only (refer to Allen & Tildesley, Computer 
> simulation of liquids, pp. 53, eqn. 2.82). For other ensembles, e.g. NVT 
> ensemble, the heat capacity should be related with the fluctuation of 
> energies.
>      Another problem: even with the energy fluctuation algorithm for the 
> heat capacity, I found it is not easy to get an convergent value. The 
> most important factor is that the fluctuations are sensitively related 
> with the temperature (pressure) coupling time constants for NVT (NPT)
> ensembles.

With a proper ensemble, e.g. NoseHoover, the time structure of the 
fluctuations is influenced by the T-coupling, but not the amplitude, 
which is what matters in the equations for heat capacity, isn't it?

> I wonder if anyone can help me resolving this problem? Thanks a lot!
> Regards,
> zgzhang
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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