On Wed, Dec 07, 2011, Jason Swails wrote:
> It appears that igb=0,eedmeth=4 does not obey the exclusion list, but
> igb=6 does. (When I add bonds, angles, and a dihedral to the system,
> igb=0,eedmeth=4 does properly exclude each atom from the non-bonded
> calculation list).
I think the code path followed by igb=0 recomputes the exclusion list based
on the bond list. This illustrates one of the dangers in
hand-modification of prmtop files: there may some hidden assumptions about
the prmtop data that are not obvious just from a description of the file
format.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 08 2011 - 05:00:03 PST
