About PME neutralization

From: B <watanabe-katsuhiro_at_hitachi-ul.co.jp>
Date: Mon 06 Mar 2000 11:42:19 +0900

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
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