From: johan strumpfer (
Date: Wed Jun 01 2011 - 11:03:04 CDT

HI Werner,

This indeed just an imaging issue. To re-wrap the output it is easiest
to use the PBCtools plugin in VMD. You can then wrap the resulting
output either by segment or by residue (see the documentation:

The cut-off that you are referring to I presume is the charmm CUTIM
parameter? If I remember correctly, this is used to set the maximum
distance for generating the pairlist. The equivalent parameter in namd
is pairlistdist. See for more info.


Johan Strumpfer:
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA

On Wed, Jun 1, 2011 at 6:09 AM, Werner Crous <> wrote:
> Dear NAMD-users
> I have a problem with imaging in NAMD. I used a truncated octahedron within
> the NVT ensemble. What happened was that after 12ns the protein only
> partially moved out of the truncated octahedron, but my one substrate was
> imaged right to the other side of the box. This then looks as if the
> substrate moved out of the protein, but I assume it is just the imaging. The
> susbstrate is imaged differently to the protein. As a CHARMM user, I know
> that one can specify if you want the imaging to happen by segment or by
> residue, but in NAMD I am not aware of such options. How does imaging work
> in NAMD for a TOH and what is the cutoff for the minimum imaging convention?
> Thank you in anticipation.
> Best regards
> Werner
> --
> Werner Crous
> Scientific Computing Research Unit
> University of Cape Town
> Rondebosch 7701
> South Africa
> Phone: +27 21 650 2530 (O)
> Fax: +27 21 686 4333

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