From: Axel Kohlmeyer (
Date: Sun Oct 21 2012 - 23:20:57 CDT

On Mon, Oct 22, 2012 at 4:00 AM, yi <> wrote:
> Axel:
> Thank you for your prompt reply. According to your suggestion, I chose
> option a, and I change dump command in lammps, dump 1 all custom 500
> id mol type xu yu zu, then in VMD Tkconsole type pbc wrap –compound
> fragment, just like you said this method can’t wrap molecules back into the

sorry, but this *can* and *does* wrap molecules back and properly so,
if the input data is proper. apparently yours isn't. so you have to
create a .psf file first and populate it with the suitable information
(element, type, mass, bond info, residue number and name).
then pbctools will work correctly.

> principal unit cell, and some molecules are still out of the box. When
> typing pbc wrap –all, all molecules are back into the box, but the molecules
> at the border are separate. Is there any method to make the unwrapped
> molecules back into the unit cell and meanwhile make the molecules at the

if you are doing it wrong, it won't work. VMD and pbctools can handle it well,
but it all depends on providing VMD with the proper information. a lammps
dump file is usually bare bones and VMD has to guess a lot and with very
few data it will guess wrong.

> border whole? In addition, the code I mentioned in the last mail may come
> from one of your courseware page 15-16. The attachments are this courseware

this is a 5 year old pdf. you should look into more recent discussions on
the VMD mailing list archives. your problem is one that is discussed often
and has been solved as many times.


> and my dump file. Could you give me some suggestion to solve this problem?
> Thanks for your help.

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.