On 7/2/12 9:54 AM, Laura Kingsley wrote:
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.
We'll probably need a better description of what you're doing, along with any
applicable figures. It sounds to me like your ligand is crashing into something
in your system, but that's just a guess based on incomplete information.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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