[gmx-users] PMF trails off to infinity.

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 2 21:42:30 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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