[AMBER] cpptraj: grid and gist

From: Thomas Fox <thomas_fox.gmx.net>
Date: Mon, 7 Dec 2015 11:22:19 +0100


   I think I stumbled over another inconsistency w.r.t. grid calculations.

   With the following cpptraj input:
   parm 2JAI_Mod_SolvIon_4Amber.top
   trajin 2JAI.nc
   parmbox 0. 0. 0.
   grid grid.dx 4 1. 4 1. 4 1. gridcenter 20. -2. 50. :WAT.O bincenter
   gist gridcntr 20. -2. 50. griddim 4 4 4 gridspacn 1. out gist.out

   I get two dx files for the water oxygen density, grid.dx (from the grid
   command) and gist-gO.dx (from the gist command)
   which I thought should produce a very similar output, as in both cases I
   calculate the same quantity.

   However, the dx headers read:
   grid.dx : origin 18.5 -3.5 48.5
   gist-gO.dx : origin 17.5 -4.5 47.5

   While the grid box definition is how I would expect it, the gist origin
   seems to be off by half a grid spacing.
   I would expect as x-values either 18,19,20,21,22 ( in case griddim refers to
   the number of grid bins - this is how I would
   understand the manual as it says "Integer number of grid increments along
   each coordinate axis")
   or 18.5., 19.5, 20.5, 21.5 (if grddim refers to the number of grid points in
   each direction which needs to
   shift by half a spacing to make up for the even number of points = uneven
   number of bins).

   Consequently, when I plot the two grids, first of all the grid boxes are
   shifted, but I also see differences in the grids;
    and more differences that I would have expected.
   For a single frame, this means that in some cases the two minima are on the
   same grid point, sometimes they
   are shifted into one direction in some cases in two directions by one grid
   For multiple frames the "structure" of the resulting grid maps looks very
   different - some of the contours (especially those
   with high occupancy) are in similar areas, but many of the contours appear
   at very different locations - is this to be expected?

   One more thing:
   In my above example, the trajectory has already been preprocessed, e.g.
   imaged and superposed. Yet, gist insists on getting
   box information, even if it is as useful as the command parmbox 0. 0. 0.

   Thanks for looking into this,
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Received on Mon Dec 07 2015 - 02:30:03 PST
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