Hi Ming,
I am not sure this is the source of your problems, but TI calculations
normally should be broken down into two steps and from what you write, Im
not sure if you do that.
First remove the partial charges on all atoms that are about to
diappear, then in a second separate simulation remove the chargeless
atoms. Otherwise you will have, especially at high lambdas, nonzero
charges on very soft atoms, which could mean another atom gets close to
them and feels a huge force, resulting precisely in the vlimit error you
mention.
Try out to break down your calculation into two steps by making a prmtop
file with all atoms still there, but zero partial charges on the ones that
will disappear, then use this as your end point of the first and starting
point of the second simulation.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Nov 18 2007 - 06:07:30 PST
