[gmx-users] 1-4 Interactions

[Mark Abraham]

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.

Mark