[gmx-users] topology error?

[Ruben Martinez Buey]

Hi David,
Thanks a lot for your reply,
The starting coordinates comes from EM, and they look like OK. If the
topology is bad, how can I check where is exactly the error?
Thanks again
cheers,
Ruben

David van der Spoel wrote:

> On Fri, 2003-01-10 at 20:01, Ruben Martinez Buey wrote:
> > Hi all,
> > IŽm testing the gromacs molecular topology of a small molecule generated
> > by PRODRG using GROMACS EM/MD. EM runs OK but MD stops just after start:
> >
> > Warning: 1-4 interaction at distance larger than 2.25
> > These are ignored for the rest of the simulation
> > turn on -debug for more information
> > Bus error (core dumped)
> >
> > How can I correct this?
> It's either the topology or the starting coordinates. Could it be a
> periodic boundary problem? (i.e. molecule split in two bits?)
>
> >
> > Thanks in advance for your kind attention,
> > with best wishes,
> > Ruben
> >
> >
> >
> >
> >
> >
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> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel,        Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576,          75123 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org  http://xray.bmc.uu.se/~spoel
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--
___________________________________________

Rubén Martínez-Buey. PhD student
Protein Function and Structure Dept. Lab. 352
Centro de Investigaciones Biológicas (CIB-CSIC)
C/ Velázquez, 144  28006  MADRID
Tlf: +34-91-561 18 00 ext. 4380
___________________________________________


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