VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Mar 20 2018 - 10:55:21 CDT

We did use OH- Chemistry&Biodiversity 2012, 9, 1019-32
with parameters developed by Ian Saam in his thesis work

francesco

On Tue, Mar 20, 2018 at 3:42 PM, Brian Radak <brian.radak_at_gmail.com> wrote:

> 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
>>
>
>