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). _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php