# Mismatch between atom numbers in index file and those reported in mdrun log file **URL:** \ **Category:** User discussions\ **Created:** [May 30, 2021, 11:52am UTC](https://gromacs.bioexcel.eu/t/mismatch-between-atom-numbers-in-index-file-and-those-reported-in-mdrun-log-file/2249 "2021-05-30T11:52:40Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![Harry](https://avatars.discourse-cdn.com/v4/letter/h/f6c823/32.png) [@Harry](https://gromacs.bioexcel.eu/u/Harry)\ **Post date:** [May 30, 2021, 11:52am UTC](https://gromacs.bioexcel.eu/t/mismatch-between-atom-numbers-in-index-file-and-those-reported-in-mdrun-log-file/2249/1 "2021-05-30T11:52:40Z")
GROMACS version:2020.3 GROMACS modification: No BS"D Tried to specify two groups for COM pulling, called END1 and END2 as follows in the index file [END1] 1 117 345 461 [END2] 109 225 237 353 But in the output file for the run GROMACS reports: pull-group 1: atom (4): atom[0]=0 atom[1]=116 atom[2]=344 atom[3]=460 weight (4): weight[0]= 1.00000e+00 weight[1]= 1.00000e+00 weight[2]= 1.00000e+00 weight[3]= 1.00000e+00 pbcatom = 116 pull-group 2: atom (4): atom[0]=108 atom[1]=224 atom[2]=236 atom[3]=352 weight (4): weight[0]= 1.00000e+00 weight[1]= 1.00000e+00 weight[2]= 1.00000e+00 weight[3]= 1.00000e+00 pbcatom = 224 So each atom number is off by one; it seems to be ordering the atoms from 0, not 1, as in the index file. Is that the way it should be? Thanks Harry ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [May 31, 2021, 1:48am UTC](https://gromacs.bioexcel.eu/t/mismatch-between-atom-numbers-in-index-file-and-those-reported-in-mdrun-log-file/2249/2 "2021-05-31T01:48:18Z")
This is normal. All arrays in GROMACS (like in all C/C++ code) are zero-based. ---
**Author:** ![Harry](https://avatars.discourse-cdn.com/v4/letter/h/f6c823/32.png) [@Harry](https://gromacs.bioexcel.eu/u/Harry)\ **Post date:** [June 2, 2021, 10:03am UTC](https://gromacs.bioexcel.eu/t/mismatch-between-atom-numbers-in-index-file-and-those-reported-in-mdrun-log-file/2249/3 "2021-06-02T10:03:46Z")
BS"D Ok, thanks Harry