[gmx-users] Re: RDF plot. This is weird!

[Lum Nforbi]

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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