[gmx-users] periodic_molecule & missing interactions

Valentina valentina.erastova at durham.ac.uk
Thu Aug 29 14:44:45 CEST 2013

I have a layered double hydroxide structure: i.e a sheet with Metals (Al &
Mg), that are balanced by OH groups on both sides. 

The sheet should be periodic in xy-direction and there are bonds between Al
and OH. 

For this, obv., I am using in-house FF, that I assign with pdb2gmx. 
In the molecule.rtp I specify bonds (Al-O, O-H) and angles (Al-O-H). There
are no dihedrals, hence nrexcl is set to 2. I also have LJ and Coulomb. 

I run energy minimisation on a small cell containing 2 layers of mineral (
1.25680  x  1.08842 x 3.20000  + angles) and get an error on 32nd step. 

May be cell is too small? 

When I run without periodic_molecule = yes I do not have such issue. 

Any help will be great! 

Step=   31, Dmax= 9.9e-02 nm, Epot=  1.95744e+08 Fmax= 3.13311e+06, atom= 64 

step 32: Water molecule starting at atom 404 can not be settled. 
Check for bad contacts and/or reduce the timestep if appropriate. 
Wrote pdb files with previous and current coordinates 
Step=   32, Dmax= 1.2e-01 nm, Epot=  1.95737e+08 Fmax= 8.74156e+05, atom=
Step=   33, Dmax= 1.4e-01 nm, Epot=  1.95706e+08 Fmax= 2.39047e+05, atom= 50 

A list of missing interactions: 
                Bond of    112 missing      4 
               Angle of    168 missing     18 
          exclusions of    535 missing      8 

Program mdrun, VERSION 4.5.5 
Source code file: domdec_top.c, line: 173 

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

"They Were So Quiet About It" (Pixies) 

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