VMD-L Mailing List

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Mar 20 2018 - 09:42:54 CDT

The standard CHARMM36 force field does not include hydroxide or hydronium.
Jana Shen's group developed a specialized force field for those molecules
to use with constant-pH MD, but I have no idea if this is recommendable for
your purposes, nor do I know how you might integrate that force field with
autoionize.

Keep in mind that "acidic" and "basic" probably do not mean what you think
they mean in this situation, since the force field has a fixed valence. I'm
not even sure you can straightforwardly compute a "pH" for your simulation
cell.

HTH,
BKR

On Tue, Mar 20, 2018 at 2:56 AM, Aman Jindal <amanjindal04711_at_gmail.com>
wrote:

> Dear all,
>
> I have a nanosheet solvated by water which I created using nanotube
> builder and solvation box in VMD. Now I would like to change few water
> molecules to hydroxide (OH) so that the system turns basic and include
> some Na+ ions to neutralize this system. How do I do it? The 'Add ions'
> tool only lets me add Na+ ions but how do I introduce OH- ions in the
> system?
>
> Thanks in advance,
> Aman
>