[gmx-users] position restrain Software inconsistency error: Some interactions seem to be assigned multiple times

[Mark Abraham]

Creighton Buie wrote:
> Hello Gromacs Community,
> 
> I am trying to set up a system where there is a coarse grained 
> hydrophobic polymer floor in a solvated water box. I am using the 
> martini force field with an .itp file for the polymer. The "floor" is 
> basically the polymer spaced 0.5 nm apart from each other and the bottom 
> bead is fixed in the X, Y, and Z direction. I have tried many ways of 
> fixing this bead using both freeze groups and position restrained 
> techniques, both to no avail. I am using PME and no part of the system 
> has a charge. The latest try has consisted of using the position 
> restrain line in the .itp file of the polymer through the topology file 
> and fixing the bottom bead with a force of 1000 in X Y Z. The energy 
> minimization run went smoothly but when I try to do any type of md I get 
> this error message:
> 
> "Not all bonded interactions have been properly assigned to the domain 
> decomposition cells
> 
> A list of missing interactions:
>            G96Angle of    432 missing      1
> 
> -------------------------------------------------------
> Program mdrun, VERSION 4.0.3
> Source code file: domdec_top.c, line: 172
> 
> Software inconsistency error:
> Some interactions seem to be assigned multiple times
> -------------------------------------------------------
> 
> "You Can Always Go On Ricky Lake" (Offspring)"
> 
> 
> 
> After searching the mailing list about this error I could only find that 
> it was a bug. Is this correct? Any suggestions is much appreciated.

If so, you should try an up-to-date version of GROMACS - 4.0.4 is current.

Mark