[gmx-users] error 1-4 interaction

[Anton Feenstra]

Maarten Wolf wrote:

> Hello,
>  
> I am running simulations on a protein/water system. Until now I used cut-off for both the coulomb as the VdW interactions. However I am wondering if the Coulomb Cut-off is appropriate for my system. So I performed a simulation using PME. It starts all fine but after app 25000 steps of 0.002 ps I get the following error message:
>  
> Warning: 1-4 interaction between 272 and 275 at distance larger than 1.9
> nm These are ignored for the rest of the simulation turn on -debug for
> more information Wrote pdb files with previous and current coordinates
> /var/spool/PBS/mom_priv/jobs/42397.ruben.SC: line 2: 17951 Segmentation
> fault      mdrun -s topol.tpr
>  
> Can anybody explain to me what this error means?

Probably your system is exploding. Look at energies and/or conformations.
You may want to increase nstener or nstxtcout, and/or set LOGBUFS = 0 to
turn of buffering of file output.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|