# [AMBER] Lennard Jones calculation

From: Antonios Samiotakis <asamiotakis.gmail.com>
Date: Fri, 11 Jun 2010 18:01:24 -0500

Hi,

I am trying to modify the 6-12 interactions for a number of non-bonded pairs
in sander.
I have located where the 6-12 force calculation takes place (my case is
eedmeth=4 in short_ene() ), but my problem is
that 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

if ( delr2 < filter_cut2 )then
icount = icount + 1
cache_x(icount) = delx
cache_y(icount) = dely
cache_z(icount) = delz
cache_r2(icount) = delr2
cache_bckptr(icount) = j
end if

Can someone give me a hint on what takes place in this routine?
While iaci and iac(j) is used for the f6 and f12 calculation in the epilogue
ew_directe.h, the calculation of delx,dely and delz
involves the indexes: n, itran. I tried printing out some of these but they
do not make any sense to me....
What is the function of the xktran, bckptr arrays?

If anyone else, has an idea on how to select and modify specific 6-12
interactions I am certainly open
to suggestions :)

Thank you,

```--
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<http://www.phys.uh.edu/%7Emscheung/Antonios.CV/Resume10.2.website.htm>
Tel: 713-743-3725
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Received on Fri Jun 11 2010 - 16:30:03 PDT
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