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
                           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.

'by removal of the average charge over the system at the beginning of
the run'

average = sum_of_charge / natom
do i=1,natom
  charge(i) = charge(i) - average

thank you.

katsuhiro watanabe
Hitachi ULSI Systems. Co.ltd
Received on Sun Mar 05 2000 - 18:42:19 PST
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