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
-
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?
Thanks
With regards
M. Kavyashree
On Tue, Jun 14, 2011 at 11:54 AM, Kavyashree M <hmkv...@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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