[gmx-users] Inconsistent shifts.
David van der Spoel
spoel at xray.bmc.uu.se
Tue Dec 18 07:51:29 CET 2007
Mitchell Stanton-Cook wrote:
> I have performed a search of the archive, but am yet to understand the
> meaning of "inconsistent shifts".
> I am using GMX331.
> I am simulating a protein structure solved by NMR.
> I have performed EM, PR and run the structure out for 500ps of MD before
> beginning my production runs.
> I am using both distance (to restrain a metal ion to a binding site) and
> orientation restraints.
> At ~4.l ns I have complaints about "2 inconsistent shifts" repeatedly in
> my log file. It suggests I check my topology.
> I am a little confused. I have another simulation exactly same
> configuration except for a larger tau_t for the time averaging length ,
> yet I have no complaints about inconsistent shifts!
> What does "inconsistent shifts" mean?
has to do with periodic boundary conditions. check where your ion is ith
respect to the protein.
anyway this should have been fixed in 3.3.2.
> Is there a way to fix this problem/ analyse what is happening?
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David van der Spoel, Ph.D.
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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