Just to expand a bit on what Jason recommended, you want to choose as
your anchor molecule something which is close to everything you want
to remain "fixed". By default cpptraj chooses the first molecule as
the anchor, but in a bilayer this may not be the best choice. you
probably want to pick a molecule that is in the center of the bilayer
as your anchor. Remember also that many actions (like radial) do their
own imaging, so imaging prior to using such commands is not necessary.
Good luck,
-Dan
On Wed, May 7, 2014 at 6:00 AM, Vijay Manickam Achari
<vjrajamany.yahoo.com> wrote:
> Dear sir,
>
> I have tried to re-image my bilayer (with water and lipids) after the simulation about 300 ns.
> I use the command "autoimage" as prescribed in AmberTools and my earlier posts.
>
> But my trials went no avail.
>
> I used commands like below, one after one in my trials in cpptraj:
>
> 1) autoimage
>
> 2) autoimage origin
>
> I also used ptraj:
> center *
> image center
>
> But all didnt work for me. I can see the bilayer shifts slowly in the box and the water molecules in one layer shift to another layer.
>
> I need you help so much.
>
> You help is very precious.
>
> Thank you.
>
> Vijay Manickam.
> Chemistry Department,
> University of Malaya,
> Malaysia
> vjramana.gmail.com
> _______________________________________________
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> AMBER.ambermd.org
> 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 Wed May 07 2014 - 08:00:07 PDT
