I have questions about energy minimization in vacuum. Since there are two force fields available, G43a1 and G43b1, I should use G43b1 for energy minimization in vacuum? What are the major difference between these two force fields?
In one previous paper (Amadei et al, 1999), a layer of water molecules were added to the surface of protein to get a closer to nature description. In this case (protein with a layer of water), which force field should I use for energy minimization, G43a1 or G43b1?
For the electrostatic interaction, I choose cut-off and infinite distances. Is this acceptable, comparing to the treatment with a distance-dependent dielectric constant?
Thank you for the help.
Lei Zhou
Columbia University
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