Hi,
> Yes, there is some problem with the system "stability", therefore I was
> trying to fix the system by restraints. Also in such case I saw unexpected
> geometry changes. I have checked the toplogy, it seems to be all right to
> me.
if your system extends beyond the virtual box, you should see it moving
around a lot when you view the trajectory, unless it is something like a
really wound up thread that unfolds. Again, that is something you should
see.
> with the change of deltaG. In following step - atoms disappearing, the non
> bonded interactions are removed. I would again expect the change of
> deltaG.
that depends on your definition of disappearing. In Amber11, that is
'removing all interactions between disappearing atoms and their
non-disappearing surroundings, while keeping intermolecular interactions
intact'. Therefore, the disappearing in vacuum leg of your cycle does not
really change anything and deltaG is zero.
> with the complete perturbation. I am just wondering if the zero value for
> deltaG is an reasonable approximation for larger molecules.
It is not an approximation, nor connected to system size. The point is
just where to put the zero point of energy, which is arbitrary and does
not influence your final 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 Thu May 26 2011 - 00:30:03 PDT
