[gmx-users] storage problem during a simulation

[Francesco]

Hi all,
This morning the gpu cluster that I'm using had some troubles with the
network connection between nodes that deny access to the storage.
Now, the simulations are still running and it seems that during the
"shut down" mdrun wrote a lot of checkpoints and restarted the
simulation once the communication was restored.

Do you think that I will have distortions or errors in the final
results?

this is a portion of the log file:

---------------- BEGIN LOG ----------------

...
DD  step 46809999  vol min/aver 0.851  load imb.: force 18.2%

           Step           Time         Lambda
       46810000    93620.00000        0.00000

   Energies (kJ/mol)
          Angle    Proper Dih.  Improper Dih.          LJ-14    
          Coulomb-14
    3.29220e+04    3.94888e+04    2.06055e+03    1.69577e+04   
    1.50705e+05
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.     
        Potential
    3.28228e+05   -2.51293e+04   -3.04153e+06    8.44070e+03  
    -2.48786e+06
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure
    (bar)
    4.98840e+05   -1.98902e+06    3.10237e+02   -2.13738e+02  
    -4.80807e+01
   Constr. rmsd
    2.76295e-05

Writing checkpoint, step 46813920 at Tue Jul 23 02:45:44 2013
Writing checkpoint, step 46813960 at Tue Jul 23 09:48:22 2013
Writing checkpoint, step 46814000 at Tue Jul 23 09:48:23 2013
Writing checkpoint, step 46814040 at Tue Jul 23 09:48:24 2013
Writing checkpoint, step 46814080 at Tue Jul 23 09:48:25 2013
...
Writing checkpoint, step 46814960 at Tue Jul 23 09:48:44 2013


DD  step 46814999  vol min/aver 0.865  load imb.: force 26.2%

           Step           Time         Lambda
       46815000    93630.00000        0.00000

Writing checkpoint, step 46815000 at Tue Jul 23 09:48:45 2013


   Energies (kJ/mol)
          Angle    Proper Dih.  Improper Dih.          LJ-14    
          Coulomb-14
    3.28615e+04    3.93530e+04    1.99727e+03    1.70754e+04   
    1.51152e+05
        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.     
        Potential
    3.30108e+05   -2.51173e+04   -3.04119e+06    8.48412e+03  
    -2.48528e+06
    Kinetic En.   Total Energy    Temperature Pres. DC (bar) Pressure
    (bar)
    4.97562e+05   -1.98772e+06    3.09443e+02   -2.13533e+02   
    3.68992e+01
   Constr. rmsd
    2.70999e-05

Writing checkpoint, step 46815040 at Tue Jul 23 09:48:46 2013

---------------- END LOG ----------------

thank you for your help

cheers,

Fra
-- 
Francesco Carbone
PhD student
Institute of Structural and Molecular Biology
UCL, London
fra.carbone.12 at ucl.ac.uk