[gmx-users] How to the define the A and B states for the calculation of free energy

Justin A. Lemkul jalemkul at vt.edu
Sun Jan 15 02:04:42 CET 2012

xu zhijun wrote:
> Thanks Justin.
> You mean I put the na+ and Ca+ in the same "moleculetype"?
> But I just worry about whether it is feasible to put the two ions in the 
> same moleculetypes even if they have no any connects between them (bond, 
> angle).

The chemical definition of a molecule and the Gromacs definition of a 
moleculetype are completely unrelated.  In theory, you could put all of the 
molecules in your system in a single moleculetype.  It's simply a topology 
construct for organization.



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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