Hi, On Thu, Jan 23, 2020 at 2:04 PM Michele Pellegrino <[email protected]> wrote:
> Hi, > > > today I was running a MD simulation and it stopped without any > error/warning message. > > It just stopped: the md.log file reported everything till the last time > step, and no information on the nature of the termination can be found in > the standard output and the standard error. > > I tried to restart the simulation using the last checkpoint but I got the > error message: > > ------------------------------------------------------- > Program: gmx mdrun, version 2019.4 > Source file: src/gromacs/fileio/checkpoint.cpp (line 2435) > > Fatal error: > Failed to lock: md.log. Already running simulation? > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > So, I double-checked if the simulation was still running in the background > (and exponentially slowed down, for some reason) or if I accidentally > stopped the process in background (without killing it, though): no trace of > the process to be found. > I run gmx energy with the default ener.edr file to see if it stopped > because of some unphysical values for the temperature or the total energy, > but everything seems to have stayed bounded. > It is actually the second time I find myself in this situation: is there > another way to what find out could have gone wrong? > > If a core file was generated , you could look at it Best regards Alessandra > > Thank you. > > > Cheers, > > Michele > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
