[gmx-users] angle constrain, constrained PF6 anion

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 1 19:00:59 CET 2011

gyorgy.hantal at 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.


> Thanks in advance.
> Gyorgy


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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