VMD-L Mailing List

From: Minjung Godfrey (minjunggodfrey_at_wayne.edu)
Date: Sat Feb 15 2020 - 17:39:49 CST

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