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

mernst at tricity.wsu.edu mernst at tricity.wsu.edu
Tue May 30 18:59:20 CEST 2006

David, I forgot to ask:

You said that

" the soft core settings that work well for the vdW portion make the charging portion a
more "difficult" transformation than normal, and the settings that work well for
charging make the vdW portion "difficult". "

What settings would you initially suggest to make the changes less difficult? Using
sc_power=1 and sc_alpha=0.5 is what you suggest for vdW changes, but what for charge
changes? Should I be using sc_power=2 and sc_alpha=1.5 to emulate older behavior? Using
sc_power=1 and sc_alpha=X.Y?

I'm also a little puzzled by the decomposition of the two calculations if I'm going to
be changing sc_power and/or sc_alpha. Should my second calculation merely add an extra
modification to the B-states (i.e. after changing atom types in B-states, I extend the
trajectory using a .top file with charge changes added to B-states) or should I use a
new topology file with my initial change placed in the A-states and only the new
(charge) changes placed in the B-states?

Thank you again for your help.

Matt Ernst
Washington State University

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