[gmx-users] gmx distance lipid bilayer

xy21hb xy21hb at 163.com
Wed Sep 30 17:18:02 CEST 2015

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.

Many thanks,



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