[gmx-users] Inconsistent shifts in g_rms

David van der Spoel spoel at xray.bmc.uu.se
Sat Feb 18 10:04:24 CET 2006

Bob Johnson wrote:
> Hello everyone,
> My system consists of an infinite carbon nanotube, water, and single stranded
> DNA.
> Whenever I run g_rms to calculate the rms displacement of the DNA or nanotube I
> get the following error message over and over again:
> There were 36 inconsistent shifts. Check your topology
Try to turn off pbc

I presume you have 36 bonds that make the CNT infinite

> It is always 36 no matter which group I pick as a reference structure. The
> program still calculates a reasonable looking rmsd function. However, I still
> wonder what this error message means and why I'm getting it. Any ideas?
> Thanks,
> Bob Johnson
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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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