Quoting Gard Nelson <[email protected]>: > Ok, here's what i've got: > > Gromacs version 4.0.5. > Both platforms are Linux, icc 10, fftw 3 > compile option: ./configure --enable-mpi >
The vast majority of Gromacs programs (read: anything not called "mdrun") are not MPI-enabled. Users have reported weird activity when using, for instance, mpicc to compile non-MPI code, although I don't know enough about that to specifically say that's the problem. I would advise following the installation instructions on the Gromacs site exactly, using MPI-enable compilers for mdrun only, to see if that fixes your issue. -Justin > thanks for your help! > Gard > > > Gard Nelson wrote: > > Hi all, > > I'm trying to simulate a solvated membrane using Berger's lipids. When > > I run grompp, i get the following error: > > > > checking input for internal consistency... > > processing topology... > > Opening library file ...lipid.itp > > Opening library file ...nb_lipid.itp > > Opening library file ...bon_lipid.itp > > Opening library file ...ff_dum.itp > > Segmentation fault (core dumped) > > > > I've tried this on two different machines with two different ff_dum.itp > > files with the same results. Moreover, I've never touched the ff_dum.itp > > file. I have modified the other forcefield files, both to include > > Berger's lipids as well as other non-standard residues. It runs fine > > with solvated proteins, but this is the first time I've run a system > > with the membrane, so i'm guessing the error is coming from there. I've > > looked through my files and cant find any errors. Does anyone have any > > ideas of what might be causing this? > > > > Lots of things. But to get better help, you'll have to provide some more > information: > > 1. Gromacs version > 2. Platform > 3. How Gromacs was compiled (commands, compilers used, etc) > > -Justin > > > Thanks > > Gard Nelson > > > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [email protected] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== -- gmx-users mailing list [email protected] http://lists.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
