[gmx-developers] Re: grompp and vsites

Michel Cuendet michel.cuendet at isb-sib.ch
Mon Jun 29 17:55:21 CEST 2009

Dear Berk and David,

Thanks for trying with my system.

Maybe energy file reading by grompp is not essential anymore, but I  
think it would be nice to keep that capability. And this kind of  
segfault may raise questions about a potential bug that could produce  
unpredicted results even when no segfault occurs...

Now on the other hand, pdb2gmx is still very essential... Has anyone  
had a chance to try and reproduce the segfault with 2guo.pdb mentioned  
in the other thread? This one is really annoying since it requires to  
build topologies by hand, one chain after the other...



On 27 juin 09, at 12:00, gmx-developers-request at gromacs.org wrote:

>> I tried
>> ~/software-4.0/bin/grompp -c confout.gro -v -e ener.edr -t
>> traj_last.trr (latest release)
>> ~/software-4.1/bin/grompp -c confout.gro -v -e ener.edr -t
>> traj_last.trr (latest git development)
>> and I have reprodced a crash in enx_names on my mac.
>> Since CVS is dead this will only be fixed in the git repository.
> If the energy file reading is the problem, it is not a serious  
> problem.
> We should have already gotten rid of the energy file reading by  
> grompp.
> Since we now have proper checkpointing it is no longer required.
> Berk

Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne

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