Dear Justin thanks for your previous explanations. We are running job with gromacs in parallel. after having the outpus of the first run, when submitting the jobs for the next 10ns we encounter with this error. can you help me to fix that. Pleas let me know the possible reasons to see this kind of error. Thanks Best wishes D. Aghaie
tarting mdrun '3840 water (TIP4P-2005) molecules' 5000000 steps, 10000.0 ps. NOTE: Turning on dynamic load balancing [HPC-0-12.local:26592] *** An error occurred in MPI_Waitall [HPC-0-12.local:26592] *** on communicator MPI_COMM_WORLD [HPC-0-12.local:26592] *** MPI_ERR_TRUNCATE: message truncated [HPC-0-12.local:26592] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) -------------------------------------------------------------------------- mpirun has exited due to process rank 2 with PID 26592 on node HPC-0-12 exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). --- On Sat, 4/16/11, Justin A. Lemkul <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] the ligand have more than one molecules To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> Date: Saturday, April 16, 2011, 3:38 AM ahmet yıldırım wrote: > Dear users, > > Is there anyone has a tutorial of the ligand have more than one molecules? Perhaps you can describe in more detail what it is you hope to accomplish. The procedure for dealing with multiple ligands is, in principle, no different from a single ligand. There are not tutorials available for every variation of a procedure. -Justin > For example: > *_topol.top:_* > [ molecules ] > ; Compound #mols > Protein_chain_A 1 > Protein_chain_B 1 > *ligandname * 3 > > Thanks in advance > -- Ahmet YILDIRIM > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists