VMD-L Mailing List

From: Brian Radak (brian.radak_at_gmail.com)
Date: Wed Mar 21 2018 - 09:15:30 CDT

At least in newer versions of VMD autoionize should permit Na, K, Ca, etc.
In any event, the procedure requires building a new PSF and PDB with the
ions and so cannot be performed without a force field (which, to my
knowledge, is hard coded in VMD).

I recently hacked this procedure myself in order to build a solution of
CaPO4, for which there is not a standard force field. I first built a box
with NaCl using autoionize and then used a series of grep and sed
procedures to split up the PDB and rename the atoms and residues to match
those for calcium and phosphate. I then fed everything back into psfgen
with a script (completely outside VMD). By the end that took maybe an hour
of work? It's not a long-term solution at all, but it met my needs. If you
want I can share the script offline.

BKR

On Wed, Mar 21, 2018 at 1:56 AM, Aman Jindal <amanjindal04711_at_gmail.com>
wrote:

> 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
>>>>
>>>
>>>
>>
>