[gmx-users] problem with intermolecular restraints

[Rebeca García Fandiño]

Dear Gromacs users,
I am trying to do a MD simulation using Gromacs 
5.1 and intermolecular restraints. I have an DNA, two peptides, a linker
 and a Ni2+ ion, and I am trying to impose intermolecular distances for 
the coordination of the Ni2+ ion with the nitrogen atoms of the linker 
and of the peptides. 

My topology file has this section:

(...)
[ molecules ]
; Compound        #mols
Protein_chain_D     1
Protein_chain_Z     1
DNA_chain_B         1
DNA_chain_A         1
UNK                 1
Ni2                 2
SOL         32360
NA               24

[ intermolecular-interactions ]
[ distance_restraints ]
;   i     j type label      funct         lo        up1        up2     weight
  2361 2416 1     0          1   0.15   0.2    0.25          1
  2360 2416 1     1          1   0.2   0.2    0.2          1
  2345 2417 1     2          1   0.2   0.2    0.2          1
  2340 2417 1     3          1   0.2   0.2    0.2          1
  438 2416 1     4          1   0.2   0.2    0.2          1
  511 2416 1     5          1   0.2   0.2    0.2          1
  134 2417 1     6          1   0.2   0.2    0.2          1
  61 2417 1     7          1   0.2   0.2    0.2          1

The simulation ended after 4 ns with this message:
(...)
Not all bonded interactions have been properly assigned to the domain decomposition cells

A list of missing interactions:
          Dis. Rest. of     16 missing      9
          exclusions of 110307 missing     -8

-------------------------------------------------------
Program gmx mdrun, VERSION 5.1
Source code file: /opt/cesga/gromacs/5.1.0/intel/15.0/gromacs-5.1/src/gromacs/domdec/domdec_topology.cpp, line: 242

Software inconsistency error:
Some interactions seem to be assigned multiple times
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Furthermore, it seems that the restraints are not working. The Ni2+ is going far away from the coordination place. 

Could anyone help me?

Thank you very much in advance.

Best wishes,

Rebeca.

Dr. Rebeca Garcia
Santiago de Compostela University
Spain