[gmx-users] implicit solvent

[Erik Lindahl]

Hi David,

>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
>constants? 
>  
>
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.

Cheers,

Erik