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Lum,<div><br></div><div>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. </div><div><br></div><div>Lastly, depending on what you are interested in, you may have better luck with a water model other than TIP3P.</div><div><br></div><div>Hope this helps,</div><div><br></div><div>Andrew</div><div><div> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div>_______________________________________________</div><div>_______________________________________________</div><div>Andrew Paluch</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Department of Chemical and Biomolecular Engineering</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">University of Notre Dame du Lac</div></div><div><a href="mailto:apaluch@nd.edu">apaluch@nd.edu</a></div><div><div>_______________________________________________</div><div>_______________________________________________</div></div></span> </div><br><div><div>On Dec 9, 2009, at 8:18 PM, Lum Nforbi wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear all,<br><br> 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.<br> 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?<br><br>Statistics over 4000001 steps [ 0.0000 thru 8000.0005 ps ], 10 data sets<br> All averages are exact over 4000001 steps<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>------------------------------<div id=":49" class="ii gt">-------------------------------------------------<br> Potential -79498.8 285.331 285.331 0.000110205 0.881641<br>Kinetic En. 14960.5 191.868 191.854 -0.0010135 -8.10799<br>Total Energy -64538.3 353.238 353.232 -0.000903288 -7.22631<br> Temperature 299.962 3.84702 3.84673 -2.0321e-05 -0.162568<br>Pressure (bar) 0.945534 194.613 194.613 0.000164281 1.31425<br>Box-X 3.94528 0.00514348 0.00514348 0 0<br> Box-Y 3.94528 0.00514348 0.00514348 0 0<br>Box-Z 3.94528 0.00514348 0.00514348 0 0<br>Volume 61.4097 0.240325 0.24032 6.42593e-07 0.00514075<br> Density (SI) 974.3 3.80629 3.80622 -1.04747e-05 -0.0837974<br>Heat Capacity Cv: 12.4748 J/mol K (factor = 0.000164481)<br>Isothermal Compressibility: 2.27095e-05 /bar<br>Adiabatic bulk modulus: 44034.4 bar</div> <br><br>Thank you,<br><br>Lum<br> <br><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">--<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<span class="Apple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div> </blockquote></div><br></div></body></html>