Hi Sara,
> Such questions have a better chance of being answered if sent to the Amber
> mailing list instead. I'm forwarding it to the list.
[...]
> I want to know when amber calculate hydrogen bonding, weather it considers
> periodic boundary condition or not since I used periodic boundary
> condition in my calculation.
just to prove Gustavo right, here is my comment:
The answer is yes, depending on what you mean:
Are you concerned about hydrogen bonds being considered during a
simulation? Amber has no special HB term, these bonds should spontaneously
form due to electrostatic interaction. Periodic boundary conditions would
apply then, as for any other force in sander.
Are you calculating hydrogen bond distributions after a simulation with
ptraj? In that case, periodic boundary conditions would also be correctly
applied, since ptraj does this implicitly for all measurements (including
Hbonds, unless I am very much mistaken and someone from the ptraj crowd
corrects me) If you want to make sure yourself, compute the Hbonds with
and without previously imaging the trajctory in ptraj, you should get the
same result.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 13 2011 - 07:30:07 PDT
