[gmx-users] radial densities

[chris.neale at utoronto.ca]

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

1. Use g_sdf from here:
http://www.gromacs.org/pipermail/gmx-developers/2006-August/001786.html

1b. With the bug fix from here:
http://www.gromacs.org/pipermail/gmx-developers/2006-August/001791.html

BUG: line 216 of 298 should have divided Y and Z by "bohr", not just X as was
previously posted. The correct line is:
fprintf(flp,"%5d%12.6f%12.6f%12.6f\n",nidxp,(MINBIN[XX]+(minx+iIGNOREOUTER)
*rBINWIDTH)*10./bohr,(MINBIN[YY]+(miny+iIGNOREOUTER)*rBINWIDTH)*10./bohr,
(MINBIN[ZZ]+(minz+iIGNOREOUTER)*rBINWIDTH)*10./bohr);

1c. With the fixed order of alignment prior to running g_sdf from here:
http://www.gromacs.org/pipermail/gmx-users/2006-August/023549.html

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).