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

[Creighton Buie]

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.

Thank you in advance,

Creighton Buie