AMBER Archive (2009)

Subject: Re: [AMBER] LJ parameters for HO and HW

From: Jason Swails (jason.swails_at_gmail.com)
Date: Sun Nov 08 2009 - 09:14:45 CST

It will behave just fine because the VDW sphere for the oxygen is large
enough to provide repulsion for that type of interaction.

On Sun, Nov 8, 2009 at 1:09 AM, manoj singh <mks.amber_at_gmail.com> wrote:

> Thanks for your reply.
>
> As you stated in your second paragraph, the L-J parameter is need for
> correct modeling of electron cloud, which include dispersion effect. But
> here, you have hydrogen with charge (some electron cloud and nucleus ) but
> no L-J parameter. Means, with a highly negative species, all attractive
> interaction but no repulsive interaction which can cause several problem
> like singularity. I am not sure how the water here will behave around a
> Glutamate or phosphate.
>
> Manoj
>
> On Sun, Nov 8, 2009 at 12:50 AM, Jason Swails <jason.swails_at_gmail.com
> >wrote:
>
> > Hello,
> >
> > The reason for HO atoms (hydrogens bonded to oxygens) have no van der
> Waals
> > radius (A and B L-J coefficients) was covered in the mailing list
> recently
> > here http://archive.ambermd.org/200910/0304.html. Atomic charges in
> amber
> > are put as point charges at the nuclear locations of each atom. Nuclear
> > locations exist regardless of whether or not an atom has a vdw sphere, so
> > these hydrogens must certainly have a charge (no hydrogen bonded to an
> > oxygen will have 0 charge), but no vdw radius.
> >
> > Also note that van der Waals potential terms and electrostatic potential
> > terms are fundamentally different. Electrostatic interactions are simple
> > coulombic interactions arising from fixed charges. VDW interactions are
> > more subtle, and are actually an empirical fit (using r^-12 and r^-6
> terms)
> > to model dispersion effects of electron "clouds" (more accurately the
> > respective orbitals of neighboring systems). Dispersion is a quantum
> > mechanical effect that arises from the correlated motions of electrons
> > which
> > is why L-J is needed at all (since simple electrostatic potentials cannot
> > capture this effect).
> >
> > Hope this helps. Good luck!
> > Jason
> >
> > On Sun, Nov 8, 2009 at 12:21 AM, manoj singh <mks.amber_at_gmail.com>
> wrote:
> >
> > > Hi all !
> > >
> > > I am having trouble in understanding why the L-J parameters for HO and
> HW
> > > is
> > > 0.00, as written in parameter file.
> > >
> > > If it is 0, then how amber manages to treat charges on it.
> > >
> > > --
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> > >
> >
> >
> >
> > --
> > ---------------------------------------
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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