Dear Amber users,
I would like to ask you if it is meaningful to run a MD simulation in
implicit water, with the purpose to compute a self diffusion
coefficient of a certain solute.
I don't think so, because implicit solvent models can not reproduce
solvent viscosity (as far as I know) and because there are not
periodic boundary conditions when using Igb.
However, I would like to read your opinions.
Thank you in advance for your advices,
Tommaso
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Received on Wed Apr 27 2011 - 02:30:14 PDT
