Hi Justin, 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).
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): For the extension from 4000 ps to 6000 ps, I have the results, Statistics over 3000001 steps [ 0.0000 thru 6000.0005 ps ], 10 data sets All averages are exact over 3000001 steps Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Potential -79499.3 288.958 288.95 -0.00126651 -7.59903 Kinetic En. 14960.4 192.23 192.206 -0.00176262 -10.5757 Total Energy -64538.9 357.576 357.538 -0.00302911 -18.1747 Temperature 299.961 3.85427 3.85379 -3.5341e-05 -0.212046 Pressure (bar) 0.925645 194.462 194.455 0.000953178 5.71907 Box-X 3.94525 0.00514608 0.00514608 0 0 Box-Y 3.94525 0.00514608 0.00514608 0 0 Box-Z 3.94525 0.00514608 0.00514608 0 0 Volume 61.4083 0.240493 0.240493 -3.12077e-07 -0.00187246 Density (SI) 974.322 3.8068 3.80679 4.31424e-06 0.0258854 Heat Capacity Cv: 12.4749 J/mol K (factor = 0.000165103) Isothermal Compressibility: 2.2742e-05 /bar Adiabatic bulk modulus: 43971.6 bar For extension from 6000 ps to 8000 ps, the results are: 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 Thanks, Lum
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