Hello,
I am using steered MD and umbrella sampling to generate a PMF profile for
pulling a small ligand 3 nm. As I pull the ligand from 3A toward 0 A, the PMF
starts a dramatic uphill climb. This does not agree with the force profile
which seems to level out. Any ideas about what might be going wrong here? I am
thinking this probably isn't correct, but I don't know where I've messed up.
Thanks! I can attach the graphs if necessary.
- Laura
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Laura Kingsley
Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643
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