I did not stop the simulation manually and it did not give a segmentation fault message, but something else that I have never seen before (and actually, I am still not understanding the error message). Now I'm running the dynamics on my machine, instead of running it on the cluster, and there are no problems at all. This means that the problem is not related to my protein or to the parameters of the dynamic, but it must be somewhere else in the mpirun command line or something like that.
grompp_mpi_d -f md.mdp -c file_pr.gro -p file.top -o file.tpr -np 32 mpirun -np 32 /dms/prog/bin/mdrun_mpi_s -s file.tpr -o file.trr -c file.gro -np 32 ----- Original Message ----- From: Mark Abraham <[email protected]> Date: Friday, February 13, 2009 10:11 pm Subject: Re: [gmx-users] Problem using MPIRUN MDRUN > [email protected] wrote: > > Thanks a lot, I'll check stderr and stdout, because I think that > the log file is correct (it looks like a normal dynamic that has > been manually interrupted). > > If you've manually interrupted the simulation, then you cannot > expect > the buffered I/O to be correctly formed. > > > The system is not exploded cause it does not generate the gro > file and step files. > > If there's no final coordinate file (.gro by default), then the > simulation did not complete correctly. > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before > posting!Please don't post (un)subscribe requests to the list. Use > the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
