Hello,
I am trying to simulate a very large protein but I am only interested in
the dynamics of only a small region of the protein that binds to an
external molecule. I was wondering if we can save an enormous amount of
computational effort by holding the entire protein completely fixed to its
original structure except for the small portion I am interested in, i.e.,
integrate the equations of motion of only those atoms belonging to this
small portion, so most of the inter-atomic forces are not even evaluated
(saving a lot of time).
I have read about belly, freeze, and shake but I believe they use some
kinds of restraints, as so it won't help in accelerating the simulation
itself.
I would really appreciate your advise on this.
Thank you!!
Sincerely,
Melisa
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 18 2016 - 12:30:04 PST
