[gmx-users] Inconsistent shifts.
David van der Spoel
spoel at xray.bmc.uu.se
Tue Dec 18 09:09:22 CET 2007
Mitchell Stanton-Cook wrote:
> Hi David,
> 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
> little deeper.
Problems reported on the mailing list tend to disappear: if you suspect
a bug please report a bugzilla.
> 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
> inconsistent shifts?
If the distance between two atoms is close to half the box, the force
may arbitrarily change sign. This is an ill-defined situation for which
there is no obvious solution.
If this is the cause of the inconsistent shifts there is not much you
can do but to check and where necessary modify the structure.
> 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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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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