[gmx-users] energy minimization in vacuum

[Lei Zhou]

Dear Gmx-users,

I have questions about energy minimization in vacuum. Since there are two
force fields available, G43a1 and G43b1, should I 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 of the
protein for NM analysis. 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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