[gmx-users] Lennard-Jones potential for protons

[Dr. Vitaly Chaban]

I am also not aware of the force field parameters for hydrated/solvated
proton, but maybe I am just wrong here.

An attempt to describe proton with Newtonian dynamics will unlikely give
you anything similar to reality. Lennard-Jones parameters play no role
here, by the way, some force fields assign zero sigma and zero epsilon to
hydrogen, for instance, in water molecule.

If you construct a particle, such as H3O+ or H5O2+, etc, it might work
somehow. But you definitely need to run some QM calculations on these
particles beforehand.


Dr. Vitaly V. Chaban




On Wed, Jul 3, 2013 at 10:00 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> One does not have a free proton in a condensed phase simulation, which
> is what all those force fields target. And even if you do, a
> classical-mechanics description of it will probably be poor at best.
>
> Mark
>
> On Wed, Jul 3, 2013 at 9:35 AM, Jong Wha Lee <jongwha12 at postech.ac.kr>
> wrote:
> > Dear Gromacs Users,
> >
> >
> >
> > Hi, I'm trying to simulate a system with a free proton included.
> However, I
> > wasn't able to find Lennard-Jones parameters for free protons in charmm,
> > amber, and opls ff. On the other hand, there are parameters for other
> > cations such as Na, K, etc.
> >
> > Is there any reason why parameters for free protons are not included? Or
> is
> > there any way I may find appropriate parameters?
> >
> >
> >
> > Thank you very much in advance,
> >
> >
> >
> > Jong Wha
> >
> > --
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