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

[Justin A. Lemkul]

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

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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