Hi,
The key thing to remember here is that what you see with imaging and what
is actually happening in the simulation can and often do look like
different things due to imaging artifacts. When your original trajectory is
imaged (i.e. iwrap=1 was used), the only way to view the non-imaged
trajectory is to use the 'unwrap' command *only*. An 'unwrap' command
followed by an 'image' command is not helpful (since 'image' re-organizes
what 'unwrap' did in the first place). If you need to re-image a trajectory
because imaging artifacts are present I first recommend that you use the
'autoimage' command in cpptraj, which takes most of the guesswork out of
re-imaging. If there still imaging artifacts after this you may need to
choose a different anchor molecule (i.e. the molecule that will be centered
and that all other molecules should be 'close' to) with the 'anchor'
keyword (by default cpptraj chooses the first molecule). Also be aware that
many commands in cpptraj (distance, watershell etc) are already
'image-aware', so re-imaging is not necessary for these commands.
Hope this helps,
-Dan
On Mon, Mar 10, 2014 at 8:18 AM, Vijay Manickam Achari <vjrajamany.yahoo.com
> wrote:
> Since I used "iwrap" command, I used "unwrap" command and reimaged the
> trajectory using commands as below:
>
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> trajin ../$system-MD300-run0900.traj 1 100 5
> trajin ../$system-MD300-run1000.traj 1 100 5
>
>
> unwrap :1-1214
> center :1-1214
> image center
> trajout abc.traj mdcrd
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>
> Can anyone advice me how to treat this trajectory files? I wish I dont
> want to repeat the simulations. It takes long time to simulation 300 ns.
>
> Hope I get solution to this problem.
>
> Thank you.
>
> Vijay Manickam Achari
>
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
> vjramana.gmail.com
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
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 Mon Mar 10 2014 - 08:00:03 PDT
