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
--
==================================================
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
[email protected] | (410) 706-7441
==================================================
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