AMBER Archive (2002)

Subject: does PME function without charge neutralization?

From: Ian R Bates (ibates_at_uoguelph.ca)
Date: Tue Apr 02 2002 - 12:30:41 CST

Hello amber users. I was wondering if it's possible to do MD with PME on
and without adding counterions (assuming you have a protein with a
charge). I tried a short simulation and it seemed to work OK but I was
under the impression that in order to use PME the system must be
neutralized. The reason I'm asking is because I wanted to do a simulation
with and without ions as a comparison, but I'm just not sure what's going
on behind the scenes.

Thanks in advance.

-Ian Bates