From: johan strumpfer (
Date: Wed Jun 01 2011 - 12:19:04 CDT

HI Werner,

This is 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: As far as I know,
namd wrap's dcd output by residue if you specify wrapAll, wrapNearest
or wrapWater (see

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.


> 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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