# Re: [AMBER] Lennard Jones calculation

From: Antonios Samiotakis <asamiotakis.gmail.com>
Date: Fri, 11 Jun 2010 20:52:50 -0500

Hi Dr. Case,

>Once you have delx, dely, delz, it should be straightforward to compute
>any function of r, and its derivatives. The "epilogue" file shows the
actual
>compution of evdw (the contribution of the LJ 12/6 terms to the energy) and
>the update to the force array.

The problem I have is exactly how to obtain delx, dely and delz for the
specified pairs I want to change.
I need to select them based on their atom index, but there is nothing in
ew_directp.h that resembles to the atom index
and I assume that I need to figure out how this is done through the indexes
I mentioned to you.

After that, doing calculations, updating the forces and so on is fine,
however I have no way to select coordinates for
the pairs I want to change and for which I need to get delx,dely and delz.

Sincerely,

Antonios

On Fri, Jun 11, 2010 at 7:48 PM, case <case.biomaps.rutgers.edu> wrote:

> On Fri, Jun 11, 2010, Antonios Samiotakis wrote:
>
> > I don't understand what takes place in the ew_directp.h file.
> >
> >
> > ! prologue: gather the data and put it in temporary arrays.
> >
> > n=ipairs(m)
> > itran=ishft(n,-27)
> > j = bckptr(n)
> >
> > delx = imagcrds(1,n) + xktran(1,itran)
> > dely = imagcrds(2,n) + xktran(2,itran)
> > delz = imagcrds(3,n) + xktran(3,itran)
> > delr2 = delx*delx + dely*dely+delz*delz
>
> Once you have delx, dely, delz, it should be straightforward to compute
> any function of r, and its derivatives. The "epilogue" file shows the
> actual
> compution of evdw (the contribution of the LJ 12/6 terms to the energy) and
> the update to the force array.
>
> It may be more difficult than this, depending on exactly what you want to
> do,
> but some of the internal manipulations are probably not relevant (?)
>
> ....dac
>
>
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>

```--
Antonios Samiotakis
Department of Physics
University of Houston
4800 Calhoun Rd
SR1 Rm 629G, Houston
TX, 77204
e-mail: asamiotakis2_at_uh.edu
http://www.phys.uh.edu/~mscheung/Antonios.CV/Resume10.2.website.htm
Tel: 713-743-3725
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Received on Fri Jun 11 2010 - 19:00:05 PDT
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