AMBER Archive (2009)

Subject: Re: [AMBER] explicit ion with igb=1

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Apr 02 2009 - 08:53:54 CDT

no, not really. if they ever dissociate they won't come back. it's possible
to restrain them to their locations, but you still need to be careful with
the solvation parameters such as radii.

in general, inclusion of explicit ions with continuum solvent should be
considered an unsolved research topic and you should read the literature
carefully.

On Thu, Apr 2, 2009 at 9:39 AM, Bala subramanian
<bala.biophysics_at_gmail.com>wrote:

> Hello,
>
> I want to simulate a DNA molecule (1kf1) with implicit solvation (igb=1).
> This molecule has few ions inherently present in the experimental
> structure.
> Can these ions be treated explicitly in such simulations. Is it correct to
> do it ?
>
> Thanks,
> Bala
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