[AMBER] distance restraints between the primary molecule and its periodic image

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Sun, 27 Jan 2013 20:22:50 +0200

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?


Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens
email: tevang.pharm.uoa.gr
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Sun Jan 27 2013 - 10:30:03 PST
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