AMBER Archive (2002)

Subject: how to neutralise the system?

From: X. Tan (xjtan_at_u.washington.edu)
Date: Mon Jan 14 2002 - 13:18:14 CST

Dear amber users,

I'd like to do some free energy perturbation work on a
pentamer with two ligands. One is neutral, and the other with one unit
negative charge. Since the pentamer has ten unit positive charges,
associating with five same ligands. If I add ten positive charges for the
first ligands' complex, then the other one still has five negative
charges. So my question is how to neutralise the whole system? I wonder
whether there is anyone having the similar experience. Any suggestions are
welcome. Thanks a lot!

Xiaojian Tan