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
[EMAIL PROTECTED]
University of Bristol, UK.
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