From: Norman Geist (
Date: Wed Mar 16 2016 - 04:52:28 CDT

PBC join uses a very expensive recursive scheme to bring together bonded
stuff and should only be used if there’s no other way around it.

For your purpose as you mentioned that you wrapped anyway, you should extend
your wrap command by two things: 1. Wrap your peptide to the center of the
cell; 2. Wrap with respect on residues. So try:


pbc wrap –all –compound res –center com -centersel protein



Norman Geist


Von: [] Im Auftrag von
Deng, Jinxia (Nancy)
Gesendet: Dienstag, 15. März 2016 21:49
Betreff: vmd-l: speed of pbc join is slow


Hi All,


I after some steps of pbc wrap, the peptide bound seems always stretch cross
the unitcell. then I use "pbc join fragment -all -verbose" .


This "join" process is super slow, 2 hrs can progress 1/4 of my trajectory
(35K atoms of peptide with membrane). So I am just wondering whether you
experienced the same, any way can speed this up??