[gmx-users] The box of umbrella sampling

Justin Lemkul jalemkul at vt.edu
Mon Oct 21 13:41:00 CEST 2013

Please keep the discussion on the gmx-users mailing list.

On 10/21/13 6:24 AM, sunyeping wrote:
> Dear professor Lemkul,
> Thank you for the reply. But I still have some questions about the umbrella
> sampling tutorial. In setion 2 of the tutorial, define the unit cell, for the
> command:
> editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box 6.560 4.362 12
> how do you know put the center of mass of the protein at 3.280 2.181 2.4775 then
> the protein will be in proper position of the box? In another word, how to
> determine the cooridnates where the COM of the protein should be put? And how to
> define the three vectors of the box. should x and y vector should always be
> twice of the x and y cooridnates following -center tag? and how to set z
> vector of the box?

By definition, the x- and y-centers have to be half the box coordinates in those 
dimensions.  The z-position was determined from an assessment of what needed to 
be done - 5 nm of COM pulling, which has to remain less than half of the box 
vector along which pulling takes place, plus some buffer for avoiding 
periodicity issues and accommodating the pulled species (in that case, a 
disordered peptide).  The defined position made all of that mathematically possible.

>         Besides, could you explain to me how to determine the angle needed to be
> rotated to make pocket channel parallel to the long axis of the box for pulling
> in umbralla sampling? With many thanks.

Presumably you can determine some vector along which pulling can be done without 
applying any rotation.  Simple trigonometry will tell you what the angle of that 
vector is with respect to the Cartesian axes.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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