[AMBER] How to prepare the two tolopogy files when doing TI calculation?

From: fancy2012 <fancy2012.yeah.net>
Date: Tue, 13 Apr 2010 20:29:17 +0800 (CST)

Dear amber users,
I want to do some TI calculation using GMX, and I have learned how to run it from the web tutorial. But there is still a problem. I don't know how to prepare the two topology files, which are initial and final states, respectively. For example, molecule A to molecule B, while the two molecules have only one different functional groups.
Could somebody give me some suggestion on it? Any response will be highly appreciated! Thanks!
All the best,
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Received on Tue Apr 13 2010 - 05:30:05 PDT
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