----- Original Message ----- From: jayant james <jayant.ja...@gmail.com> Date: Thursday, September 30, 2010 9:36 Subject: [gmx-users] distance restrained D simulations To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> > Hi! > I am trying to perform distance restrained MD simulations of a protein with > Gromacs4.0.5. > I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am > incorporating simular to NOE distance restraints in NMR. The details of how you tried to do this are important. See http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm and consider section 5.4 of the manual. There might be a solution that does not have this issue. Mark > When I use one processor for the simulations its all fine, but, when I use > multiple processors I get a bunch of errors > lets me start with the "NOTE" found below. Well do not want to increase the > cut-off distance but want the program to use multiple processors. How can I > overcome this problem? > I would appreciate your input > Thanks > JJ > > NOTE: atoms involved in distance restraints should be within the longest > cut-off distance, if this is not the case mdrun generates a fatal error, in > that case use particle decomposition (mdrun option -pd) > > > WARNING: Can > not write distance restraint data to energy file with domain decomposition > > Loaded with Money> > > > ------------------------------------------------------- > Program mdrun_mpi, > VERSION 4.0.5> Source code file: ../../../src/mdlib/domdec.c, line: 5873 > > > Fatal error:> There is no domain decomposition for 4 nodes that is compatible > with the given box and a minimum cell size of 8.89355 nm > Change the number > of nodes or mdrun option -rdd or -dds> Look in the log file for details on > the domain decomposition > > -------------------------------------------------------> > "What Kind Of Guru > are You, Anyway ?" (F. Zappa) > > Error on node 0, will try to stop all the > nodes> Halting parallel program mdrun_mpi on CPU 0 out of 4 > > gcq#21: "What > Kind Of Guru are You, Anyway ?" (F. Zappa)> > > -------------------------------------------------------------------------- > > mpirun has exited due to process rank 2 with PID 28700 on> node > compute-3-73.local exiting without calling "finalize". This may > have caused > other processes in the application to be> terminated by signals sent by > mpirun (as reported here). > > -------------------------------------------------------------------------> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > with > errorcode -1.> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > processes. > You may or may not see output from other processes, depending > on> exactly when Open MPI kills them. > > --------------------------------------------------------------------------> > > > > > > > > -- > Jayasundar Jayant James > > www.chick.com/reading/tracts/0096/0096_01.asp) > > -- > 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
