[gmx-users] Re: data points missing

[Kavyashree M]

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 <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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110614/32f15069/attachment.html>