Hi AMBER users.
I think a neutralization of a system containing a protein is a VERY VERY
important problem. So I want to know the meaning of next statements.
--------------------------------------------------------------from Manual
ISCHARGED
Standard use is to have ISCHARGED = 0
which forces neutralization of the unit
cell by removal of the average charge over
the system at the beginning of the run.
[This is necessary due to the roundoff
error associated with the parm derived
charges (upon reading in a parameter file,
the sum of the charges for a neutral sys-
tem does not sum to zero).] When
ISCHARGED = 1, the unit cell is not neu-
tralized. Technically, the Ewald summa-
tion method is not correct when a non-
neutral system is used (energy will
change, independent of the direct sum tol-
erance, but the forces are still correctly
determined). However, the method has been
applied for non-neutral systems and may be
useful for equilibrating systems in the
absence of counterions, for example.
---------------------------------------------------------------------------
Does
'by removal of the average charge over the system at the beginning of
the run'
mean
"
average = sum_of_charge / natom
do i=1,natom
charge(i) = charge(i) - average
enddo
"
?
thank you.
katsuhiro watanabe
Hitachi ULSI Systems. Co.ltd
Received on Sun Mar 05 2000 - 18:42:19 PST
