gyorgy.han...@fc.up.pt wrote:
Dear all,
I am setting up a simulation of ionic liquids with the PF6 anion.
According to the potential, the anion should be kept rigid, wich
obviously means that bond lengths and angles have to be constrained.
LINCS doesn't work with angle constraints (i.e. constraing a triangle),
so we decided to use SHAKE. However, SHAKE seems to work a bit
strangely: I know SHAKE mustn't be used with domain decomposition, but
even if I set the corresponding variable to NO in the mdp file, the
simulation crashes on 8 procs and gives the following error message:
Fatal error:
1 particles communicated to PME node 7 are more than a cell length out
of the domain decomposition cell of their charge group.
If I try to run mdrun with -pd (to 'really' switch off domain
decomposition), the simulation doesn't chrash but gives nonsense (the
energy seems to increase constantly).
I am not an expert user so maybe I do something wrong but, anyway, does
anyone have an idea how to constrain this anion with Gromacs? I checked
mailing list archive but couldn't find any answer corresponding to my
question.
Without seeing a complete .mdp file, it's not possible to fully diagnose this
problem. The combination of SHAKE + particle decomposition should be stable,
but there are a whole host of different things that can go wrong.
-Justin
Thanks in advance.
Gyorgy
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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