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 <hmkv...@gmail.com
<mailto: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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