Hi,
This sounds like an imaging artifact. Try the 'autoimage' command in
cpptraj to center and re-image the system and see if that improves the
look of the simulation.
Imaging is really both a visual convenience and a way to ensure
coordinates do not overflow during very long simulations. If you don't
want imaging to occur during your simulation you can set 'iwrap=0' in
your input; if you do this I also recommend you use NetCDF
trajectories and restarts (ioutfm=1 and ntxo=2 respectively) since
these will not overflow as quickly as their ASCII counterparts.
Also note that the 'unwrap' command in cpptraj can reverse imaging.
Hope this helps,
-Dan
On Wed, May 21, 2014 at 7:47 AM, Ilias Patmanidis
<patmanidis.ilias.gmail.com> wrote:
> Dear AMBER users,
>
> I was running MD simulations of a system with two peptides. After the
> simulation, I noticed that the system was moving towards and over the
> boundaries of the cell and the generated trajectory had the two peptides in
> different locations of the water box.
>
> Is there any way to move one of the peptides to its relative position
> regarding the other peptide? Or could you suggest me a way to avoid this
> result in future simulations?
>
> I thank you in advance.
>
> Greetings,
> Ilias
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--
-------------------------
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 21 2014 - 07:30:02 PDT
