[gmx-users] Inconsistent shifts in periodic molecules
adeyoung at andrew.cmu.edu
Thu Apr 19 03:54:01 CEST 2012
I am a little embarrassed to ask this, especially because there are many
posts related to the term "inconsistent shift." Unfortunately, I still
cannot seem to find the answer to my question.
What is an inconsistent shift? Is it related to constraints or restraints?
Or is it more related to the coordinates of the atoms?
My system is an infinite graphene sheet. I am using periodic_molecules =
yes, so that the slower periodic boundary condition algorithm is used. In
my .itp file for graphene, I specify bonds that do cross the boundaries of
the box (atoms on the left side are bonded to atoms on the right side; atoms
on the top are bonded to atoms on the bottom). And similarly for the angles
and dihedrals: in my .itp file, I specify angles and dihedrals that cross
the boundaries of the box.
grompp and mdrun run with no error or warning messages. But when I run
analysis tools like g_traj, g_spatial, g_potential, and g_rdf, I get error
"There were 130 inconsistent shifts. Check your topology"
My question is, could these inconsistent shifts cause errors and
inaccuracies in my analyses? The consensus on old mailing posts seems to be
"maybe" -- depending on the analysis, inconsistent shifts could cause
inaccuracies. But, my question is, is there anything that I can do to debug
these inconsistent shifts, or to conceptualize ahead of time whether the
accuracy of my analyses are likely to be adversely affected? I have checked
my .itp file for graphene, and my assignment of the bonds, angles, and
dihedrals look correct (_assuming_ that it is legal to specify bonds,
angles, dihedrals, constraints, etc. which cross periodic boundaries, like a
bond between an atom on the left side of the box and an atom on the right
side of the box, since the molecule is periodic/infinite). Is there
anything else in particular that I can look for to try and diagnose the
Thank you kindly!
Carnegie Mellon University
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