[gmx-users] Umbrella Pulling

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 13 14:11:53 CET 2012

Steven Neumann wrote:
> Dear Gmx Users,
> Is it always required to restrained positions of the protein while 
> pulling your ligand? My system is made of 10 ligands attached to my 
> protein surface. I am pulling one of them.

No, it is not required.  I assume you've gotten this idea from my tutorial - the 
restraints there were used for a very specific purpose (detailed in the paper 
linked from the tutorial).

> I have just seen trajectory of pulling my ligand without restraining 
> positions of protein and 9 remaining ligands. My ligand while pulling 
> also pulled the protein with itself (for 1 nm distance) and then 
> splited. Is is this approach more reliable?

If your goal is umbrella sampling, you need only generate a series of reasonable 
starting configurations along a defined reaction coordinate.  The absolute 
positions are irrelevant; it is the relative distance that matters.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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