[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 01:33:52 CET 2012

xu zhijun wrote:
> Hi gromacs-users,
> I have carefully checked the manual about the define the A and B states 
> for the calcualtion of free energy. And I also known that 
> "couple-moltype“ and "couple-lambda0" and "couple-lambda1".
> However I have two types of molecules for decoupling in the simulaiton. 
> It seems that Gromacs can not deal with more than one tpes of moleucle 
> with the "couple-moltype".
> For example I want to decouple the Na+ and Ca+. Is the the other way to 
> define the decoupling molecules? It seems that I can directly define the 
> B state in the top files for these two ions, repectively. If it is 
> reasonable, does the other molecules without the descrption of the B 
> state keep fixed? (I mean these molecuse will not involve the decoupling 
> process in the simulation.)

If there is not a defined B-state, then parameters from the A-state are applied, 
hence no transformation.  Another approach is to hack the topology such that the 
ions you want to decouple are all in the same [moleculetype].



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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