[gmx-users] Inconsistent shifts.
s4026869 at student.uq.edu.au
Tue Dec 18 09:00:43 CET 2007
Using GMX3.2.2 unfortunately introduces more problems. See my message on
the 10/08/2007. I recently came across a post suggesting this is due to
a error in Reaction Field, however I believe that this problem me be a
I have come across inconsistent shifts before - it corresponds to when
the metal ion crosses a PBC. I think the conclusion I came to last time
after some investigation was that I should not worry? Do these
inconsistent shifts affect my simulations ? However, this time I am a
little uncertain. Partly due -
Distance restraints were used to co-ordinate the metal ion. I also
created a pseudo-bond between the metal ion and a single co-ordinating
residue. This was due to what I believe to be a problem in the
orientation restraints code. I found that when the metal crossed the PBC
the orientation tensor "both grew and fluctuated" by large orders of
magnitude. I concluded that this was due to PBC not being handled
correctly. Since the introduction of the pseudo-bond there have been no
problems. Given that the metal ion is now by definition part of the
protein, PBC should not be an issue and I should not be seeing
David van der Spoel wrote:
> 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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