VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Dec 21 2011 - 08:25:16 CST

On Tue, Dec 20, 2011 at 10:23 PM, Yu Zhou <zylp2006_at_gmail.com> wrote:
> Hi there,
>
> I'm trying to simulate divalent ion binding in the cytosolic domain of
> the BK channels. It seems that the CHARMM force field and the VMD
> Autoionize plugin only support a very limited set of divalent ions. Is
> there any way to add ions such as Cd2+ and Ba2+ in the system?

adding them is easy. the problem is that it is *really* difficult
to get meaningful results from simple classical MD.
divalent ions cause strong polarization of their immediate
neighborhood while at the same time being partially
neutralized through "back donation" from the surrounding
water molecules. that effect is practically impossible to
model with regular force field (with constant charges).

so if you can come up with a good way to model this,
all you'd have to do is to insert some other divalent
cations and then rename them suitably afterwards.

cheers,
    axel.

>
> Your input is highly appreciated.
>
> Yu Zhou 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.