[gmx-users] Inconsistent shifts Problem when using g_rdf

David van der Spoel spoel at xray.bmc.uu.se
Fri Jan 16 09:06:43 CET 2009

Lin, Pohan wrote:
> 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?

Probably, yes. I think it will go fine in version 4.0 though. Please 
wait until 4.0.3 before upgrading.

> Thanks,
> Po-Han
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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