AMBER Archive (2002)

Subject: Re: does PME function without charge neutralization?

From: darden (darden_at_gamera.niehs.nih.gov)
Date: Tue Apr 02 2002 - 16:23:02 CST

Dear Ian
If you don't run a neutralized system, amber will substitute a uniform
neutralizing plasma for the missing counterions. Thus the system is always
neutral.
Hope this helps
Tom Darden
 On Tue, 2 Apr 2002, Ian R Bates wrote:

> 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
>
>
>