[gmx-users] PMF trails off to infinity.

Laura Kingsley lkingsle at purdue.edu
Mon Jul 2 21:53:44 CEST 2012

Basically what I'm doing is pulling a ligand toward a dummy atom. I pull 
the ligand until its COM is very close (a few angstroms) from the dummy 
atom. Could this be causing this behavior? What information would help? 
I'm having a tough time getting the figures attached but may be I could 
email them directly to you? Let me know.


- Laura

On 07/02/2012 03:42 PM, Justin A. Lemkul wrote:
> 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

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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