[gmx-users] How to prepare the two tolopogy files when doing TI calculation?

[fancy2012]

Dear GMX users,
I want to do some TI calculation using GMX, and I have learned the tutorial of TI calculation from this web site http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial.
So I have know how to run TI calculations. But there is still a problem. I don't know how to prepare the two topology files, which are initial and final states, respectively. Could somebody give me some suggestion on it? Any response will be highly appreciated! Thanks!
 
All the best,
Qinghua 

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