[gmx-users] segmetation fault and inconsistent shifts

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 8 09:29:40 CET 2005

liu xin wrote:
> Dear gmx-users;
> When I tried to minimize my lipid/protein system I got a "segmetation 
> fault" error message and the mdrun program stopped, then I  checked the  
> em.log file found there was a warning "There were 2 inconsistent shifts. 
> Check your topology". Did this warning cause the stop?.
> I searched this forum and did as told before: to add a line "pbc = xyz" 
> to my em.mdp, and export GMXFULLPBC = 1. But I still got this two 
> messages. I started the mdrun like $/home/xin/program/.../mdrun, and I 
> export like $export GMXFULLPBC, did I do it in a wrong way? My system is 
> SUSE 9.0, GMX 3.1.4, I am new to GMX and Linux, could anybody so kind 
> tell me how to over come this problem?
please upgrade gromacs
> Thanks in advance!
> Liu Xin
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
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://xray.bmc.uu.se/~spoel

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