Hi,
As far as I know there is a way to do this; to my knowledge, the
distance restraints in Amber have no concept of periodic image. In any
case I don't think adding artificial restraints to your system to
avoid clashes between images is the right thing to do. Unless there is
some reason why your system needs to have a certain size, ideally the
size of your unit cell should be large enough so that these clashes do
not occur.
-Dan
On Sun, Jan 27, 2013 at 11:22 AM, Thomas Evangelidis <tevang3.gmail.com> wrote:
> Dear AMBER users,
>
> I would like to know if distance restraints between the protein in the
> primary cell and one of its periodic images are allowed. The C-terminal
> loop of my protein interacts at some point of the simulation with the
> N-terminus of the protein in a periodic cell, and stays there for a long
> time. To avoid that I would like to apply a force that moves away the
> C-terminal loop whenever it reaching a cutoff distance from the periodic
> image. Is this possible in AMBER?
>
>
> thanks,
> Thomas
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
> _______________________________________________
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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) 585-9119 (Fax)
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Received on Sun Jan 27 2013 - 15:00:02 PST
