Re: making force grids

From: Thomas Brian (
Date: Wed Jun 20 2012 - 23:08:24 CDT

To update my question in case anyone else has similar questions:

-the order of grid points is as I expected, with zindex being the inner

-its going to be difficult to replicate NAMDs lennard jones force
approximation unless you know how they implement their lookup tables

Also, in the .dx file format, you do no include the brackets that are in
the example. My fprintf line is just:
object 3 class array type double rank 0 items %i data follows

Also, I don't know if it matters, but I just left the last line of my grid
data with however many grid pts were left over, so my last line of grid pts
might have 1 or 2 or 3 data pts.

On Wed, Jun 13, 2012 at 6:36 PM, Thomas Brian <>wrote:

> Hello,
> 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)
> Thanks,
> Tom

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