[gmx-users] Re: data points missing

[Mark Abraham]

On 14/06/2011 6:09 PM, Kavyashree M wrote:
> Dear users,
>
>      gmxcheck on the .xtc file shows that simulation has run for 100ns
> but while calculating energy terms using ener.edr file, it gives "nan" 
> error -

Sounds like you have managed to calculate only on a subset of your data. 
I'm guessing that g_energy reports the RMSD as calculated from a 
quantity that is updated as the simulation progresses, and when the 
input file you're using doesn't correspond to the whole time interval, 
that quantity computes wrongly.

>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Temperature                     300      9e-05       -nan 
> -0.000501989  (K)
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Pressure                    0.99914      0.027       -nan  0.0174391  
> (bar)
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Volume                      517.755     0.0094       -nan   0.010871  
> (nm^3)
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Density                     1012.53      0.018       -nan -0.0216399  
> (kg/m^3)
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Kinetic En.                  129266      0.039       -nan  -0.216264  
> (kJ/mol)
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Potential                   -710705         62       -nan   -394.425  
> (kJ/mol)
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Total Energy                -581438         62       -nan   -394.641  
> (kJ/mol)
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Coul-SR:Protein-Protein    -26868.2         97       -nan   -674.338  
> (kJ/mol)
> Coul-14:Protein-Protein     28921.7        9.1       -nan    47.6164  
> (kJ/mol)
> Coul-SR:Protein-non-Protein   -27393.6        160       -nan    
> 1050.26  (kJ/mol)
> Coul-14:Protein-non-Protein          0          0       -nan          
> 0  (kJ/mol)
> Coul-SR:non-Protein-non-Protein    -742644         92       -nan   
> -622.378  (kJ/mol)
> Coul-14:non-Protein-non-Protein          0          0       
> -nan          0  (kJ/mol)
>
> an number of data points is only  1978700 compared to actual data points
> of 5000001. where could be the error? and is it possible to get the 
> missing data
> points?

You can't get the missing data from the file from which it is missing. 
Whether you have any other files is something only you know.

Also, 5000000 data points from 100ns is collecting data far too often 
for most purposes. Quantities from adjacent time steps are strongly 
correlated, and gathering extra data points that are highly correlated 
with existing data points gains correspondingly little.

Mark

> Thanks
> With regards
> M. Kavyashree
>
> On Tue, Jun 14, 2011 at 11:54 AM, Kavyashree M <hmkvsri at gmail.com 
> <mailto:hmkvsri at gmail.com>> wrote:
>
>     Dear users,
>
>        In one of the simulations I have run, I have transfered
>     it from one system to another so some data points were missing
>     what I should do now. how to find which data points are missing?
>
>     Thank you
>     With regards
>     M. Kavyashree
>
>

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