Lum Nforbi wrote:
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).
I would disagree. The default method of RDF calculation is by atom (see g_rdf
-h, specifically the -rdf flag!), as RDF are often plotted between pairs of atom
types (O-O, O-H, H-H in the case of water). Try again using a proper
calculation method.
-Justin
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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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