[gmx-users] 1-4 interaction, infinite meanings for energies

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 5 15:51:22 CET 2009

drugdesign wrote:
> Dear GROMACS users,
> I've got a warning during equilibration molecular dynamics with TIP3P solvent (amber03  force field):
> Warning: 1-4 interaction between 2 and 21 at distance 5.887 which is larger than the 1-4 table size 2.000 nm
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size.
> What can be the reason for this?

There are many.  This error is reported to the list several times per month, if 
not more often.  Search the list archives, and read here:



> I've got infinite meanings of temperature and energies and MD run seems to nag up (or maybe it's just very very slow?)
> Can this be caused by non-zero charge of the system?
> I've tried to add ions to the .tpr file and then to use resulted PDB file for new cycle of minimization and molecular dynamics, but the problem remanis. Here are two logs of MD runs - wth and without water.
> Best regards,
> Andrew
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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