On 21/08/2012 2:30 PM, Yun Shi wrote:
Hello all,
I am simulating protein-ligand complex with amber99sb force field in
TIP3P water. What would be a reasonable value rvdw? I saw someone
uses 1.0, and I did not find any abnormality when using 1.4 nm for
rvdw, but where can I find the right reference?
It's cited in the GROMACS manual. Of course, you read it, and reports of
similar studies others did with the force field before choosing
it,right? :-)
And is this force field parameterized with or without dispersion
correction? (Better to turn it on or off?)
Generally, one should follow the parametrization strategy, unless/until
someone shows that observables relevant to yours are unaffected or
improved by a change.
Mark
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