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
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