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.
[email protected] http://folding.bmc.uu.se
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