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

[Justin A. Lemkul]

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
> 

-- 
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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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