[gmx-users] 1-4 Interactions

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 19 09:35:33 CEST 2006

toma0052 wrote:
> Hello,
>      I am starting simulations on a DPPC lipid bilayer taken from Peter
> Tieleman's website.  Upon trying to run the energy minimization, the
> program runs, but the results does not appear correct.  During the run, I
> get the warning:
> Warning: 1-4 interaction between 908 and 913 at distance 1.621 which is
> larger than the 1-4 table size 1.000 nm.  These are ignored for the rest of
> the simulation.  This usually means your system is exploding, if not, you
> should increase table-extension in your mdp file.
> I have tried increasing the table-extension in my em.mdp file, but I need
> to increase it to over 10nm in order for that error to go away.  Could
> someone explain a little bit more on what the table-extension and 1-4
> interactions are, and what could possibly be wrong with my energy
> minimization.  All I have done so far is to take the dppc128.pdb file and
> the example2.top topology file from Peter Tieleman's site, run editconf and
> grompp with en em.mdp file similar to John Kerrigan's tutorial, followed by
> mdrun.  Any help would be appreciated.

My guess is the topology is broken, or doesn't correspond to the 
configuration. Get out VMD or something and look at things visually.


More information about the gromacs.org_gmx-users mailing list