[gmx-developers] Re: grompp and vsites
David van der Spoel
spoel at xray.bmc.uu.se
Tue Jun 30 00:40:23 CEST 2009
Michel Cuendet wrote:
> 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...
I tried it with OPLS/AA or Charmm and get
Chain identifier 'A' was used in two non-sequential blocks (residue 602,
Is this the error you are getting as well? It doesn't crash for me.
> 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.
> Michel Cuendet, Ph.D
> Molecular Modeling Group
> Swiss Institute of Bioinformatics
> CH-1015 Lausanne
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David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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