From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
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.

https://github.com/jhenin/qwrap

On Sat, Feb 15, 2020 at 7:05 PM Minjung Godfrey <minjunggodfrey_at_wayne.edu>
wrote:

> 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
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin