[gmx-users] storage problem during a simulation

[Mark Abraham]

gmxcheck can still read your output files safely. :-)

On Tue, Jul 23, 2013 at 10:26 PM, Francesco <fracarb at myopera.com> wrote:
> the simulations are still running, they should end tomorrow afternoon.
>
> Fra
>
> On Tue, 23 Jul 2013, at 06:26 PM, Mark Abraham wrote:
>> What does gmxcheck have to say about your output files?
>> On Jul 23, 2013 12:17 PM, "Francesco" <fracarb at myopera.com> wrote:
>>
>> > 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
>> > --
>> > gmx-users mailing list    gmx-users at gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > * Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-request at gromacs.org.
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> Francesco Carbone
> PhD student
> Institute of Structural and Molecular Biology
> UCL, London
> fra.carbone.12 at ucl.ac.uk
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists