[gmx-users] Inconsistent shifts Problem when using g_rdf

[Lin, Pohan]

I am running NPT simulations by using Parrinello-Rahman pressure coupling on Gromacs 3.3.3.  My system contains epoxy and cross-linker molecules.  By modifying the topology file (add bond, angle, torsion terms in topology), all the molecules are connected together to be an huge polymeric molecule.  The MD jobs were running well before and after polymerization.  However, while analyzing the data by using g_rdf,  it keeps showing the message "There were XXX inconsistent shifts.  Check your topology" for the structures after polymerization and the g(r) are not reasonable.  Does anyone have any idea about this issue?   I am also curious about how g_rdf deal with "inconsistent shifts."  Does g_rdf ignore those data or do something else?

Thanks,
Po-Han
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