[gmx-users] Re: TI, sampling, sc_power, and sc_alpha

[mernst at tricity.wsu.edu]

David and Berk,

I enormously appreciate your help in diagnosing my free energy problems. Berk, when you
said "I had implemented the alpha=1 option in 3.3 and set it as default" I presume you
mean the sc_power=1 option, yes? David, when you talk of splitting the vdW and charge
mutations into separate stages, you mean initially (for example) setting the B-states to
have only altered atom types (and hence vdW radii), then later extending the
trajectories generated in each window while using a new .top file that also has altered
charges in the B-states -- right?

Again, thank you for your help in handling this tricky topic.

Matt Ernst
Washington State University