Re: [AMBER] correct way of imaging for rdf

From: Daniel Roe <>
Date: Thu, 23 Jan 2014 10:27:11 -0700


On Thu, Jan 23, 2014 at 9:52 AM, Jio M <> wrote:

> I tried to see restart file generated using cpptraj its same. Broken I
> mean to say : the broken part is on the opposite side of box so just image
> periodicity issue

Have you tried using other molecules as the 'anchor' molecule? For example:

autoimage anchor :253-269

As I said before, cpptraj by default uses the first molecule as the anchor,
but if that molecule is not 'central' to all other solute molecules then
autoimage may not work as expected. If you want, send me (off-list)
topology/restart files (or even a mol2) and I can make a more specific

> >> No worries here - unless you specify 'noimage' to 'radial', imaging is
> done for you
> So I dont need to do image traj first and then do RDF analysis? Also
> imaging is done by default for other analysis as well, like distance etc.?

No, as I said the 'radial' command images distances by default. The
'distance' command does as well unless 'noimage' is specified. The manual
states whether a command performs imaging by default or not so I recommend
you read the manual carefully. For example, the 'hbond' command does not
perform imaging.

> But what kind of imaging done by default? As I see autoimage if I do
> manually it does not work and even if it works my molecule is not in center
> of box

Re-imaging for visualization and imaging distances are two different
procedures. When re-imaging for visualization (e.g. the autoimage command)
you are re-centering the trajectory on a molecule of interest, then
re-imaging everything that may now be outside the unit cell back into the
unit cell. It doesn't always work because autoimage is essentially trying
to guess what the final picture should look like. Imaging distances (e.g.
the distance command) is a more basic procedure; you are just trying to
find the shortest distance between two points in periodic space, which
*always* works. So even if the visualization looks 'broken', imaging is
always done correctly internally so the 'radial' command will work just

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jan 23 2014 - 09:30:03 PST
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