Lum,
You'll have better luck if you perform a few simulations at different
temperatures at the same pressure and mole number, and then
numerically differentiate the resulting enthalpy. I believe that the
default heat capacity that Gromacs will print out is only valid for
NVE simulations, and I am not sure of the formulas that you are
referring to from Allen and Tildesley & J.M. Haile. Also, don't
expect your calculated heat capacity with TIP3P to agree the
experimental value. You should under-predict the experimental value.
Lastly, depending on what you are interested in, you may have better
luck with a water model other than TIP3P.
Hope this helps,
Andrew
_______________________________________________
_______________________________________________
Andrew Paluch
Department of Chemical and Biomolecular Engineering
University of Notre Dame du Lac
[email protected]
_______________________________________________
_______________________________________________
On Dec 9, 2009, at 8:18 PM, Lum Nforbi wrote:
Dear all,
I have run an 8 ns NPT simulation of 2000 molecules of TIP3P
water and I have a very low Cv value of 12.4748 J/mol K (factor =
0.000164481). The result is below. I ignored this value and have
tried using formulas for Cv that I found in the two books: Allen
and Tildesley & J. M. Haile but I can't come out with the right
answer.
Has anyone ever calculated Cv or Cp for water manually from
scratch and gotten the right answer? If so, please, could you give
me the details of what you did?
Statistics over 4000001 steps [ 0.0000 thru 8000.0005 ps ], 10 data
sets
All averages are exact over 4000001 steps
Energy Average RMSD Fluct.
Drift Tot-Drift
------------------------------
-------------------------------------------------
Potential -79498.8 285.331 285.331
0.000110205 0.881641
Kinetic En. 14960.5 191.868 191.854
-0.0010135 -8.10799
Total Energy -64538.3 353.238 353.232
-0.000903288 -7.22631
Temperature 299.962 3.84702 3.84673
-2.0321e-05 -0.162568
Pressure (bar) 0.945534 194.613 194.613
0.000164281 1.31425
Box-X 3.94528 0.00514348 0.00514348
0 0
Box-Y 3.94528 0.00514348 0.00514348
0 0
Box-Z 3.94528 0.00514348 0.00514348
0 0
Volume 61.4097 0.240325 0.24032
6.42593e-07 0.00514075
Density (SI) 974.3 3.80629 3.80622
-1.04747e-05 -0.0837974
Heat Capacity Cv: 12.4748 J/mol K (factor = 0.000164481)
Isothermal Compressibility: 2.27095e-05 /bar
Adiabatic bulk modulus: 44034.4 bar
Thank you,
Lum
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