From: Axel Kohlmeyer (
Date: Sun Jan 03 2016 - 11:17:49 CST

On Sun, Jan 3, 2016 at 11:53 AM, Morteza Jalalvand <>

> Dear developers,
> In mergemols and selections2mol procedures (in topoutils.tcl), the box of
> the new molecule is considered to be the largest of the available of boxes
> (ie by setting a, b, and c to max of each molecule's a, b, and c) which is
> necessary but not sufficient. If two molecules have the same a, b, c but
> one of them is displaced relative to the other the box found by these
> procedures can't contain both of them.
> This could cause problems in writelammpsdata procedure of topolammps.tcl
> where cell dimensions found by min/max search are overridden by this
> incorrect box.

​true, but this is the result of a limitation in VMD​, which does not store
the origin of a box, but only its dimensions. so for topotools it is not
possible to know whether atoms are outside of a box due to PBC unwrapping
or displacement of the entire box. it assumed the former, as that is the
more common case when writing out LAMMPS data files.

the only thing that could be done in topotools would be to never set the
box dimensions after those merge operations, but that would be inconvenient
in case the two merged systems share the same origin.

in short, the basic rule "never trust automated procedures" applies. thus
in your case, you should manually (or via script) determine what is a
reasonable choice for the box dimensions and reset it to those parameters
before writing out the topology and geometry to a LAMMPS data file. since
you do know what operations you perform, you know what the box is supposed
to be and that is much better than having topotools guess for you.


> Regards, Morteza

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.