Mismatch between atom numbers in index file and those reported in mdrun log file

User discussions
1

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

2

This is normal. All arrays in GROMACS (like in all C/C++ code) are zero-based.

3

BS"D

Ok, thanks

Harry