Dear all: I just test the tutrial ( http://www.dillgroup.ucsf.edu/group/wiki/index.php/Free_Energy:_Tutorial) and my own system, and I fond somthing confused me: If I understand correct, when lamda is 0 (all atoms on), there should be no difference between trun on or turn off soft-core potentional. In addition, there should be no different whatever you set the sc-alpha value. However, I've test the methane system on both gromacs 4.0.4 and 3.3.3, and found when lamda is 0, you get different large result when sc-alpha were set to 0, 0.5 and 1.5. I wonder has any one notice this before or I misunderstood the formula?
Yours Jia
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