[gmx-users] Inconsistent shifts using multiple bonds type 6

TJ Piggot t.piggot at bristol.ac.uk
Mon Mar 5 19:15:19 CET 2007

Hello all,

I am trying to apply a set of harmonic distance restraints between pairs of 
protein atoms in my system, which is protein/ligand/water/ions in a 
periodic box.

The way i am doing this is to use the bond type 6 and to add these bonds at 
the end of the [bonds] section in my topology file, after the system has 
been energy minimised and i have performed position restrained MD, without 
these harmonic distance restraints.

I can then run it through grompp with no problems and start mdrun. If i 
only have a few (ie less than about 30) harmonic distance restraints then 
the simulation if fine and runs happily. However if i increase the number 
of restraints then mdrun crashes due to lincs warnings and it also says 
that the are inconsistent shifts, (the number of inconsistent shifts varies 
depending on which atoms i choose to restrain and also the number of atoms 
chosen) a warning not seen with less harmonic distance restraints.

I should also say that i have run this system without these harmonic 
restraints without problems for tens of nanoseconds already. Also this 
problem can be repeated if i try to use the [distance_restraints] however 
it requires less restraints to get the inconsistent shift warning (and 
lincs problems) this way.

If anyone can give me an idea of what is causing this problem it would be 
warmly appreciated, or even just how to detect which of the harmonic 
distance restraints will cause the problem before i run mdrun so i can 
replace the problem 'bonds' in the topology file.

Thanks for any advice you can give

Tom Piggot

TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.

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