Hello, I'm using ffoplsaa with a new atom type (Ag) that I've included in the .atp file, LJ parameters I've specified in the nb file. My system topology I've written by hand in an itp file. The problem is that after any kind of run the molecule penetrates the metal surface! This shouldn't be happening. I had been using g45a3 quite successfully for the same system and everything was working fine. Do I need to do something different/special with oplsaa? What am I missing?
Advice appreciated, Chris Rowan
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