[gmx-users] g_dist tools

[Poncho Arvayo Zatarain]

Hello, i want to run this command: echo "3 4"| g_dist -f dppc128_1-nj-ct-nobox.xtc -
s dppc128_1.tpr -o dppc128-Dpp.xvg -n Dpp.ndx -b 20000 in Gromacs 5.0.4 but when i run it, the following appears: This tool has been removed. Please see tool changes for 5.0. And when i see th tools appears: 
g_dist: This tool has been removed in 5.0. A replacement is gmx distance (for most options) or gmx select (for -dist or -lt).If you had index groups A and B in index.ndx for g_dist, you can use the following command to compute the same distance with gmx distance:gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' -oxyz -oall
The -intra switch is replaced with -nopbc.


If you used -dist D, you can do the same calculation with gmx select:

gmx select -n index.ndx -select 'group "B" and within D of com of group "A"' -on/-oi/-os/-olt
You can select the output option that best suits your post-processing needs (-olt is a replacement for g_dist -dist -lt)


Shoukd i use -dist or -intra option?