From: Axel Kohlmeyer (
Date: Thu Sep 20 2012 - 07:50:35 CDT

Please note that mergemol combines VMD molecules with no regard for their coordinates. If you want to multiply your system use replicatemol. Axel.
Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

-----Original Message-----
From: kirtana S <>
Date: Thu, 20 Sep 2012 01:13:47
To: <>
Subject: vmd-l: Use of topotools

Dear VMD users,

While trying to create a box of 4 different kinds of atoms in a box in
different proportions I am using the scripts provided by topotools

After I define the three different type of atoms in similar ways as
provided by the script for hexane/cyclohexane in the tutorials. Use of
mergemol command for more than one repetitions also repeats the similar
coordinates so I cannot have number of similar molecule selections i.e
::TopoTools::mergemols [list $mol1 $mol2 $mol2 $mol3 $mol1 ]

Can you suggest a way of modifying the script to have ratio of mixture
as something other than 1:1