Dear all,<br><br>I am trying to calculate Cv of a pure alkane 125 molecules with actual density, and here is what I have done:<br><br>
<p class="MsoNormal">1- <br></p><p class="MsoNormal"><br></p><p class="MsoNormal">Cv: Run NVT > g_energy>select T and Etot=total energy</p>
<p class="MsoNormal">As I issue g_energy <span> </span>*.edr
</p>
<p class="MsoNormal">Heat Capacity Cv:<span>
</span>12.4787 J/mol K (factor = 0.000369503)</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">And when I choose –nmol XXX <span> </span></p>
<p class="MsoNormal">Heat Capacity Cv:<span>
</span>13.4007 J/mol K (factor = 0.0462137)</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">- Do I have to use –nmol? What would be the unit with –nmol ? <br></p><p class="MsoNormal"><br></p><p class="MsoNormal">and as I issue g_energy using 4.5.3 <br></p><p class="MsoNormal"><br></p><p class="MsoNormal">
Temperature dependent fluctuation properties at T = 299.987. #constr/mol = 0<br>Heat capacity at constant volume Cv: 341.734 J/mol K</p><p class="MsoNormal"><br></p><p class="MsoNormal">and with -nconstr # of bonds<br>
</p><p class="MsoNormal"></p><p class="MsoNormal"><br></p><p class="MsoNormal">Temperature dependent fluctuation properties at T = 299.987. #constr/mol = 19<br>Heat capacity at constant volume Cv: 262.746 J/mol K<br><br>
- From this I am guessing what 4.0.7 reports is not correct!? </p><p class="MsoNormal"><br></p><p class="MsoNormal">but still what I am getting from 4.5.3 is far from actual reported value (around 170). I guess I am missing something..! or Is the difference acceptable? <br>
</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"> g_energy says:</p>
<p class="MsoNormal">you will need to give the number of constraints per molecule
–nconstr</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">- so I need to count how many bonds are fixed in the molecule as
I am setting constraints= all-bonds?</p><p class="MsoNormal">The way to this is counting no. of bonds? What about macromolecules? Is there an easier way of finding number
of constraints?</p>
<p class="MsoNormal"> </p><p class="MsoNormal">2-</p><p class="MsoNormal"><br></p><p class="MsoNormal">Cp:</p><p class="MsoNormal"><br></p><p class="MsoNormal">I did NPT, g_energy *.edr -nmol XXX -nconstr (4.5.3)</p><p class="MsoNormal">
I want to select T and enthalpy but since enthalpy is not on the list I select total-energy (which is Etot I think) and pv terms but g_energy is still giving Cv!<br></p><p class="MsoNormal"><br></p><p class="MsoNormal">Property Energy terms needed<br>
---------------------------------------------------<br>Heat capacity Cp (NPT sims): Enthalpy, Temp <br></p><p class="MsoNormal"><br></p><p class="MsoNormal"><br></p><p class="MsoNormal">Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Total Energy 86.1571 0.085 1.55565 -0.0944531 (kJ/mol)<br>Temperature 300.074 0.07 5.77219 0.318146 (kJ/mol)<br>
pV 15.8128 0.061 1080.82 -0.249203 (kJ/mol)<br><br>Temperature dependent fluctuation properties at T = 300.074. #constr/mol = 19<br>Heat capacity at constant volume Cv: 325.067 J/mol K<br>
<br></p><p class="MsoNormal">Can you please guide me where the problem lies?</p><p class="MsoNormal">-------------------------------------------------------</p><p class="MsoNormal"><br></p><p class="MsoNormal">again Cv : to compare with constraints=none</p>
<p class="MsoNormal">but still -nconstr should be on otherwise I values are more off. <br></p><p class="MsoNormal"><br></p><p class="MsoNormal">Total Energy 132.418 0.051 1.77314 0.144794 (kJ/mol)<br>
Temperature 300.008 0.052 4.50209 0.15866 (kJ/mol)<br><br>Temperature dependent fluctuation properties at T = 300.008. #constr/mol = 20<br>Heat capacity at constant volume Cv: 442.016 J/mol K<br>
<br></p><p class="MsoNormal"></p><p class="MsoNormal"><br></p>
3- <br><br>Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp<br>Isothermal compressibility: Vol, Temp <br>Adiabatic bulk modulus: Vol, Temp <br><br><br>Since volume appears for calculation of the above properties , does this imply only NPT results in these properties?<br>
<br>and wanted to make sure what 4.5.3 reports is reliable..<br><br><br>Many thanks for you time!<br><br>Best,<br>