[gmx-users] heat capacity etc.

[David van der Spoel]

On 2011-03-09 19.48, Thomas Koller wrote:
> Hello,
>
> I want to calculate the isobaric heat capacity, the thermal expansion coefficient and the isothermal compressibility:
>
> i) My value for the heat capacity (NPT) is very low. I used option -nmol. Whan can be the reason or is the calculation of this property not accurate with this tool? By the way, why is there always written c(v) although I analyze a NPT run c(P)?
>
Did you use a thermostat that yields a canonical ensemble?
The best way to compute the Cp is from the fluctuations in the enthalpy.
Note that the quantum corrections / constraint corrections are not 
correct. We are working on a better method.
> ii) How can I obtain the thermal expansion coefficient from the NPT run, I can't see it? The isothermal compressibility is calculated.
>
 From g_energy -h:

Some fluctuation-dependent properties can be calculated provided the correct
energy terms are selected. The following properties will be computed:
Property                        Energy terms needed
---------------------------------------------------
Heat capacity Cp (NPT sims):    Enthalpy, Temp
Heat capacity Cv (NVT sims):    Etot, Temp
Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
Isothermal compressibility:     Vol, Temp
Adiabatic bulk modulus:         Vol, Temp
---------------------------------------------------



> Regards,
> Thomas


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se