[gmx-users] gmx distance lipid bilayer

Justin Lemkul jalemkul at vt.edu
Wed Sep 30 17:20:40 CEST 2015

On 9/30/15 11:17 AM, xy21hb wrote:
> Dear all,
> I am using gmx distance to calculate the distance between the center of mass (c.o.m.) of the phosphorous group (PO4, 5 atoms)
> and the c.o.m. of the lipid bilayer system in Justin's tutorial (a typical lipid DPPC bilayer system) by issuing, as shown on GROMACS website for gmx distance,
> gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' -oxyz -oall -s md.tpr -f md.trr
> where A = Phsphorous B = System.
> The distance should be about the chain length of the lipid, so ~ 20 A
> However, it gives ~ 0.1 nm. I just wonder why it is like that.

Because your assumption is wrong.  The bilayer is centered in the box, so the 
COM distance between the center of the system and the center of the P atoms is 
usually about the same position, so you get a value that is nearly zero.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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