On 12/29/13, 8:17 AM, Andrew Bostick wrote:
Dear gromacs users

I know g_dist tool calculates the distance between the centers of mass of
two groups of atoms as a function of time.

How to obtain average distances of the selected atoms form the bilayer
midplane. In this case, one group is selected atoms, but another group?


If you are interested in the bilayer midplane, then selecting the entire bilayer as the other group is appropriate.

Is g_dist appropriate for this case? How?


If you are not interested in the exact COM distance, but instead the distance between the group and the midplane, then looking only at the z-component of the COM distance seems to make sense, given that you would be uninterested in the x- and y-components of the distance, if the membrane is in the x-y plane.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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