From: Giacomo Fiorin (
Date: Sun Feb 16 2020 - 12:30:19 CST

Hello Minjung, "pbc unwrap -compound fragment" (or "qunwrap compound
fragment" - see link below) would be the way to go, but you should
ensure that the fragment IDs are correctly assigned. Verify this with:
set sel [atomselect top all]
$sel get fragment
If you don't get the same fragment ID for all the atoms inside one POPC
molecule, you need to either use something else, e.g. "-compound residue"
or tell VMD how to get the correct fragment IDs based on how your system is
set up and the file format you use.

On Sat, Feb 15, 2020 at 7:05 PM Minjung Godfrey <>

> Hi,
> I have a bilayer membrane with POPC with which I'm trying to study the
> average diffusion rate of individual molecule. Basically, I need to unwrap
> all, get the center of mass for each molecule, and calculate the average
> diffusion coefficient of all molecules. When I unwrap it, some molecules
> get stretched or cut. When it is wrapped, molecules on the boundary get cut
> (part of the molecule appears on the other side of the box). "-compound
> fragment -all" does not keep the molecules intact either. Is there a way to
> keep the individual molecule intact as they jiggle around the edge? How can
> I keep it whole and only jump to the other side of the box when, say, half
> the molecule drifts across one boundary?
> Thank you!
> Minjung Godfrey

Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD