Hi all,
In my MD simulation I have specified a bellymask in which I want
"All the atoms within 80 angstroms of the residue 324 to move except for
the residues 999-1039".
So the way I have specified it is
ibelly=1,bellymask= '(:324 <.80.0) & !(:999-1039)',
But after 79 picoseconds the simulation stops due to an ammonia molecule
dashing out of the structure and the distance between the ammonia that is
coming out and the residue 324 is 111 angstroms. While I have given a
constraint like above how can a molecule wander 111 angstrom away from the
residue 324? Is there something wrong with the way I have specified the
bellymask?
I really appreciate your suggestions to understand what I have done wrong.
Thnak you
Sajeewa Dewage
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 15 2012 - 17:00:02 PST
