[gmx-developers] Re: grompp and vsites

[Tsjerk Wassenaar]

Hi Berk e.a.

When the reading of energy files with grompp is terminated, it will no
longer be possible to use it to properly handle runs started with
versions prior to 4. It doesn't seem to hurt to keep it, right?

Cheers,

Tsjerk

On Mon, Jun 29, 2009 at 5:55 PM, Michel
Cuendet<michel.cuendet at isb-sib.ch> 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...
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623