AMBER Archive (2009)

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

From: manoj singh (mks.amber_at_gmail.com)
Date: Sun Nov 08 2009 - 00:09:13 CST

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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> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> ---------------------------------------
> 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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