Hi,
On Wed, Feb 5, 2014 at 4:22 AM, Jio M <jiomm.yahoo.com> wrote:
> trajin temp.nc
> center origin :1-254 # (these are all residues)
> image origin center familiar
> trajout temp_image.rst restart
>
> Structure looks fine and protein channel seems to be in center of
> octachedron. I want to analyse ions in protein channel. Would this be fine?
> Any suggestions will be really helpful.
>
Your re-imaging problem is slightly easier than most since your initial
trajectory is not imaged, meaning there are no imaging artifacts to begin
with (which is typically what makes re-imaging difficult and is what
'autoimage' is primarly designed to help correct). The input you provided
looks fine to me; however, be aware that if any of your molecules are moved
out of the box by your centering they will be 'wrapped'. Also, if your box
size is small you could end up with solute molecules at box edges switching
back and forth from one side to the other, which may not be what you want.
It can't hurt to visualize your re-imaged trajectory to make sure no
artifacts have been introduced.
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Feb 05 2014 - 13:00:03 PST
