making force grids

From: Thomas Brian (
Date: Wed Jun 13 2012 - 18:36:00 CDT

I would like to replace a large group of fixed atoms by the field they
impose on the mobile atoms using Force-grids. Is their an easy way to do
this? Do I need to rewrite the NAMD lennard jones implementation in my own
code, or perhaps someone has already done this say in VMD scripting, or
matlab? Thus i could just move an imaginary test particle around my grid
and have it compute the potential at each point.

I am confused by some wording in the manual regarding the layout of the
force-grid file. I need to express a 3D grid as a 1D string of numbers. I
do not know what you mean be "fast dimension". If my potential function is
U(xi,yi,zi), what is the order of the indexes that I need to loop over? I
would guess
for xi=1..xn
  for yi=1..yn
    for zi=1..zn
       print U(xi,yi,zi)


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