[gmx-users] The box of umbrella sampling

[Justin Lemkul]

On 10/20/13 9:13 AM, sunyeping wrote:
> Dear gromacs users, I am studying gromacs umbralla sampling. I want to pull a
> lingand out of its binding pocket in a protein. By observing the
> ligand-protein complex, I think I should pull the ligand along a direction
> which is not parallel to the x, y or z axis so as to prevent the ligand
> colliding with the atoms around the the pocket. So I have to define a box
> whose long axis is parallel to the pulling direction. Could anyone explain to
> me that how to define the box?Thanks in advance!

You don't define the box around the solute, per se, but you orient the solute 
within the box.  Simple rotation with editconf -rotate should align your active 
site channel with a Cartesian axis.

-Justin

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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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