Hi,
I want to simulate bulk small organic molecules, and using GAFF and sqm I created the topology for a test system (dimethoxy ethane). Lets say after running constant pressure simulation, the density doesn't converge to the experimental value, could the problem be the partial charges, or is it the force constants?
Another question I have is, is there a certain cutoff that I should use for vdw? I know usually it is between 8 to 12, but is there a rule of some sort to choose this? If the parametrization use a particular cutoff, is it safe to change the cutoff for my molecule?
Farid Ismail
Graduate Student
Dept. of Chemistry/Biochemistry
University of Oklahoma
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Received on Mon Aug 08 2011 - 14:30:03 PDT
