[gmx-developers] Re: grompp and vsites

[David van der Spoel]

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

Fatal error:
Chain identifier 'A' was used in two non-sequential blocks (residue 602, 
atom 6295)

Is this the error you are getting as well? It doesn't crash for me.
> 
> Thanks,
> 
> Michel
> 
> 
> 
> 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
> Switzerland
> http://ludwig-sun1.unil.ch/~mcuendet/
> ==========================================================
> 
> 
> 
> 
> 
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-- 
David.
________________________________________________________________________
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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