[gmx-users] Problems with calculating Cv and Cp

[Andrew Paluch]

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
apaluch at nd.edu
_______________________________________________
_______________________________________________

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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