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?
Cheers
Mitch
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