[gmx-users] using OH ions in combination with CHARMM27 force field

[Justin Lemkul]

On 12/10/15 12:29 PM, soumadwip ghosh wrote:
> Thanks Justin for your reply. I was wondering then how to prepare an OH.itp
> file from the scartch. Can it be made using pdb2gmx? Also from some old

It's already in ions.itp; you don't need to create anything.

> threads I came accross that hydroxide and hydroxonium ions are species
> which dont obey classical dynamics. I would appreciate your thoughts on
> this.
>

Classical MD is not a very good approach for studying pH-dependent behavior, and 
there is little to be gained by trying to simulate these fixed models of OH- or 
H3O+.  The actual physics involved are far more complex than a fixed charge, 
fixed protonation model can ever convey.

The OH- parameters were derived using in vacuo water interaction energies, but 
AFAIK were not validated against free energy of solvation, interactions with 
ions, etc. so I am not sure how suitable they are for what you're doing.

> I would also like to know if I make an NaOH.itp somehow and then add it to
> my system containing the polymer is it going to behave like a
> polyelectrolyte? Sorry if I am asking much.
>

Your polymer will behave however your topology dictates.  If it's got ionized 
residues, isn't that the definition of a polyelectrolyte?  Not really my field.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================