[gmx-users] Tabulated potentials make newbies crazy

Justin A. Lemkul jalemkul at vt.edu
Sun Nov 29 17:10:15 CET 2009

ms wrote:


Sorry to say I can't help with the larger problem, but I'd like to comment on this:

> The problem is that since I have a single molecule now, and the single
> molecule must be neutral, so it must be all a single charge group
> ("Therefore we have to keep groups of atoms with total charge 0
> together. These groups are called charge groups.", 4.6.2).

Your interpretation of charge groups is incorrect.  A protein is a single 
molecule, as well, isn't it?  We define numerous charge groups in a protein. 
What really matters is that suitably-sized functional groups (generally 3 to 4 
atoms) are contained within a charge group, such that the charge group 
(typically) carries a net integral charge (-1, 0, +1, etc).



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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