[gmx-users] radial densities

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Sep 6 09:53:06 CEST 2006

Can't think of a current program that does this. One option is to:

1. Use g_sdf from here:

1b. With the bug fix from here:

BUG: line 216 of 298 should have divided Y and Z by "bohr", not just X as was
previously posted. The correct line is:

1c. With the fixed order of alignment prior to running g_sdf from here:

trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none
trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans

This will give you the spatial distribution function... not quite what you want. 
However, you could easily write a bash script that converted this spatial 
distribution function into an all-helix radial distribution function (if I am 
correct that you intend to derive a single plot with radial distance on the x 
axis and a density-given-x over the y axis).

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