[gmx-users] topology error?

[David van der Spoel]

On Fri, 2003-01-10 at 20:01, Ruben Martinez Buey wrote:
> Hi all,
> I´m 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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