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

xu zhijun simulationxu at yahoo.com
Sun Jan 15 01:24:32 CET 2012

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.)

Thanks very much for any suggestions
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