[gmx-users] segmetation fault and inconsistent shifts

liu xin zgxjlx at gmail.com
Thu Dec 8 08:53:02 CET 2005

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.logfile 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?

Thanks in advance!

Liu Xin
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