VMD-L Mailing List

From: Aman Jindal (amanjindal04711_at_gmail.com)
Date: Wed Mar 21 2018 - 00:56:31 CDT

Actually, my question is about how to just model the system in VMD and not
regarding force fields for hydroxide ions. Since the 'Add ions' tool in
VMD only allows to add Na+ ions but how do I introduce OH- ions in the
system?

On Tue, Mar 20, 2018 at 9:25 PM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> 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
>>>
>>
>>
>