[gmx-users] implicit solvent
lindahl at stanford.edu
Thu Nov 7 18:48:44 CET 2002
>Being educated in the home of water simulations, I am obviously doubtful
>toward implicit solvent... What does this say about all the protein
>folding simulations in implicit solvent trying to estimate rate
You cannot estimate a rate constant without a viscuous term that applies
to atoms facing vacuum. The Pande group
developed such an integrator, have no idea about others.
But again - I'm not too enthusiastic about implicit water for folding
dynamics - once you add the viscuous drag
you might as well use explicit water since it isn't going to be any
faster :-) The main reason we are working on it
here at Stanford is that it would be nice as a discrimination function
for ab initio Monte Carlo stuff.
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