Dear Amber Users:
I've been using NPT ensemble to run a long polypeptides, then after
centering the water to the "primary box", I found that both my chain ends
are out of the box. My concern is whether the hydrogen bonds calculation
will accurately reflect the really number of hydrogen bonds, since I'm
analyzing the post trajectory with water already centered.
If not, will the only thing I can do is to increase my buffer to a much
larger number and rerun the simulation? I'm not sure whether ptraj or
cpptraj will consider the constant pressure and volume change when they are
doing the analysis? Or do they just use the water in the primary box to
calculate it?
Thanks!
Binwu
--
Binwu Zhao
Dept of Chemical and Biomolecular Engineerig
NCSU
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 12 2013 - 21:30:02 PDT
