[gmx-users] RE: heat capacity etc. (Thomas Koller)

[David van der Spoel]

On 2011-03-12 14.00, Thomas Koller wrote:
> I dont know exactly what you mean. Here you can see my output data:
>
>
> Energy                      Average    RMSD    Fluct.  Drift  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                 -48.8499  1.82144  1.81841 -0.00781553  -0.3638
> Kinetic En.                50.7548  1.42996  1.42991 -0.000872827 -0.0406286
> Total Energy               1.90489  2.32653  2.3236  -0.00868836  -0.404429
> Temperature                298.15   8.40003  8.39975 -8.84014e-05 -0.238666
> Pressure (bar)             1.66395  713.24   713.236  0.00302056   8.15491
> Volume                     21.0391  0.179301 0.178412-2.2873e-05 -0.0617527
> pV                        -0.45227  903.541  903.536  0.00377916   10.203
> Heat Capacity Cv:      13.3969 J/mol K (factor = 0.0460384)
> Isothermal Compressibility: 3.71208e-05 /bar
> Adiabatic bulk modulus:        26939.1  bar
>
> i) How should I calculate the isobaric heat capacity with this values, bu udage of the Fluct. in the 3rd column?
>
> ii) How is the isothermal compressibility here calculated?
>
> Regards,
> Thomas
You have to read up, check Allen & Tildesly or something like that.

To get the enthalpy you have to extract the total energy graph and and 
the volume graph and sum Etot + p time Volume (in xmgrace or excel, 
whatever). Then compute the fluctuations from that. You have to do it 
all manually.

The heat capacity above is meaningless, this is why we have improved 
that in newer gmx version. Note that if you have used Berendsen T and/or 
P coupling you can not compute any fluctuation properties from your 
simulations.

-- 
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