[gmx-users] angle constrain, constrained PF6 anion

gyorgy.hantal at fc.up.pt gyorgy.hantal at fc.up.pt
Tue Feb 1 18:33:15 CET 2011

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.

Thanks in advance.


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