Hi Justin,<br><br> I chose my whole system of 2000 water molecules. I discussed this plot with someone and they said that rdf can be plotted for atoms as well as whole molecules and that the shape of my rdf plot was not a problem of my having used the whole system (I am not really sure about this).<br>
<br> The length of my run was 8 ns (8000 ps). The energy values don't change much so I think the system is pretty equilibrated. I have included below the results of my last two run continuations of 2000 ps each (I had to extend the run to ensure equlibration):<br>
<br><span style="color: rgb(51, 51, 255);">For the extension from 4000 ps to 6000 ps, I have the results,</span><br><br>Statistics over 3000001 steps [ 0.0000 thru 6000.0005 ps ], 10 data sets<br>All averages are exact over 3000001 steps<br>
<br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>Potential -79499.3 288.958 288.95 -0.00126651 -7.59903<br>
Kinetic En. 14960.4 192.23 192.206 -0.00176262 -10.5757<br>Total Energy -64538.9 357.576 357.538 -0.00302911 -18.1747<br>Temperature 299.961 3.85427 3.85379 -3.5341e-05 -0.212046<br>
Pressure (bar) 0.925645 194.462 194.455 0.000953178 5.71907<br>Box-X 3.94525 0.00514608 0.00514608 0 0<br>Box-Y 3.94525 0.00514608 0.00514608 0 0<br>
Box-Z 3.94525 0.00514608 0.00514608 0 0<br>Volume 61.4083 0.240493 0.240493 -3.12077e-07 -0.00187246<br>Density (SI) 974.322 3.8068 3.80679 4.31424e-06 0.0258854<br>
Heat Capacity Cv: 12.4749 J/mol K (factor = 0.000165103)<br>Isothermal Compressibility: 2.2742e-05 /bar<br>Adiabatic bulk modulus: 43971.6 bar<br><br><span style="color: rgb(51, 51, 255);">For extension from 6000 ps to 8000 ps, the results are</span>:<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>-------------------------------------------------------------------------------<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<br>
<br>Thanks,<br>Lum<br>