Dear users, <br> <br> gmxcheck on the .xtc file shows that simulation has run for 100ns<br>but while calculating energy terms using ener.edr file, it gives "nan" error - <br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Temperature 300 9e-05 -nan -0.000501989 (K)<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Pressure 0.99914 0.027 -nan 0.0174391 (bar)<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Volume 517.755 0.0094 -nan 0.010871 (nm^3)<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Density 1012.53 0.018 -nan -0.0216399 (kg/m^3)<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Kinetic En. 129266 0.039 -nan -0.216264 (kJ/mol)<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Potential -710705 62 -nan -394.425 (kJ/mol)<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Total Energy -581438 62 -nan -394.641 (kJ/mol)<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Coul-SR:Protein-Protein -26868.2 97 -nan -674.338 (kJ/mol)<br>Coul-14:Protein-Protein 28921.7 9.1 -nan 47.6164 (kJ/mol)<br>
Coul-SR:Protein-non-Protein -27393.6 160 -nan 1050.26 (kJ/mol)<br>Coul-14:Protein-non-Protein 0 0 -nan 0 (kJ/mol)<br>Coul-SR:non-Protein-non-Protein -742644 92 -nan -622.378 (kJ/mol)<br>
Coul-14:non-Protein-non-Protein 0 0 -nan 0 (kJ/mol)<br><br>an number of data points is only 1978700 compared to actual data points<br>of 5000001. where could be the error? and is it possible to get the missing data<br>
points? <br><br>Thanks <br>With regards<br>M. Kavyashree<br><br><div class="gmail_quote">On Tue, Jun 14, 2011 at 11:54 AM, Kavyashree M <span dir="ltr"><<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Dear users,<br><br> In one of the simulations I have run, I have transfered<br>it from one system to another so some data points were missing<br>
what I should do now. how to find which data points are missing?<br><br>Thank you<br>
With regards<br><font color="#888888">M. Kavyashree<br>
</font></blockquote></div><br>