From: Simon Dürr (
Date: Fri Sep 11 2015 - 15:42:26 CDT


I still have some problems using ILS in VMD. After generating the ILS
run script with PBC enabled it yields only volumes in one corner of
the search box. I suspect the alignment to be the problem. In the
paper (Imaging the Migration Pathways for O2, CO, NO, and Xe Inside
Myoglobin) and the book chapter (Finding Gas Migration Pathways in
Proteins Using Implicit Ligand Sampling) it appears that the authors
are aligning (rot+trans) the trajectory before using the ILS tools.
However, reading the comments and help texts in volutil it is
suggested to not align prior to volmap if PBC is used:

“If you use -pbc DO NOT ALIGN the frames of the structure yourself
prior to the calculation! It will totally mess up the definition of
your PBC cells. Instead you should use the -alignsel option and let
volmap handle the alignment ….“

Using the PBC option the generated ILS run script consists of an
alignment step for the translation only (ILStools::shift_to_center
$asel) followed by pbc wrap and finally alignsel is used in volmap.
Could anyone elaborate on the use of ILStools::shift_to_center $asel
and how it affects alignsel? In addition, should I use an aligned
trajectory before executing the ILS run script?

In my case the only alignment I see was done by
ILStools::shift_to_center $asel since all volumes in the DX file are
in the corner to which my system was aligned by shift_to_center. So
instead of having the entire system aligned on top of frame 0 the
system shifts out of the search space.

The simulation I'm using has 10000 frames for 10ns.