VMD-L Mailing List

From: shiladitya_at_jncasr.ac.in
Date: Sun Aug 10 2008 - 10:52:54 CDT

Hello ,

i am using VMD to see configurations stored in .xyz file.
i want to put the see the configuration with the simulation box . i am
trying to use the 'pbctools' package.

the commands given on tkconsole (after loading the single-configuration
xyz file) are:

package require pbctools
set molid [molinfo top]
set cell {9 10 30 41 136 124}
molinfo $molid set {a b c alpha beta gamma} $cell
pbc box -on

it does show both the configuration and the simulation box.

but the problem is, the simulation box has different orientation than the
configuration, that is the atoms in the configuration are not inside the
box as they should be.

how to fix this?

thanks in advance,

shiladitya