[gmx-users] Re: Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)

[Mark Abraham]

Arun kumar wrote:
> Hi Tsjerk and others,
>                     I tried to simulate one surfactant and one
> chloride ion in 500 waters and got similar type of errors. I mean my
> system got collapsed for l-bfgs minimization and for steepest descent
> the potential energy is a large number.(obviously some bad contacts).
> It seems the problem is with topology. Earlier I asked about what is
> meant by broken topology?? Can anyone tell what may ne the problem and
> also about what is meant by broken topology??

A broken topology is where you haven't managed to describe the bond 
connectivity in your .top file that you'd like to. The way to fix it is 
to reduce your problem to its simplest form (single surfactant in 
vacuum, as David suggests), observe where the breakage occurs, read 
chapter 5 carefully, and remedy appropriately.

Mark