On 09/02/10 09:04, Justin A. Lemkul wrote:
Quoting Gard Nelson<gardnersnak...@gmail.com>:
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.
A quicker diagnostic may be whether grompp works on other simulation
systems.
Also, inspect this ff_dum.itp for well-formedness. Try commenting out
its #include and see what breaks then.
Mark
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
jalem...@vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
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