Indexing issue and grompp

GROMACS version: 2021.2
GROMACS modification: No
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I have indexing issue in the xtc file format.
my top file has the following items:

; Compound      #mols
IAUM           18642
protein        XXXX; i have intentionally changed the Proteins to XXXX
W           3798848
NA               1714

in the mdp file, I try to just output my NP, protein and ions in the xtc file:

nstxtcout                = 10000  ; Output frequency for .xtc file
xtc_precision            = 100
xtc-grps                 =IAUM-Pro-ion ;IAUM protein IONs_all

to do so, I make a group in my index file called “IAUM-Pro-ion”. I also double checked to make sure the index numbers do match and I only have IAUM, protein and ION in the system!

However, when I try to use trjconv to convert xtc to gro file, using the same index file and the same group as shown below ( Group 18 ( IAUM-Pro-ion) has 444023 elements ), I get error of mismatching numbers.

gmx trjconv -f nvt-production-30fs.xtc -s nvt-production-30fs.tpr -o nvt-production-30fs-c.gro -pbc mol -n index.ndx 
                     :-) GROMACS - gmx trjconv, 2021.2 (-:

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GROMACS:      gmx trjconv, version 2021.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/mkhatami/uoft/gromacs/Au-C6-1ao6-1hzh-1d3k/all-elastic/full-structures/80nmbox/006-nvt-production-large-freeze
Command line:
  gmx trjconv -f nvt-production-30fs.xtc -s nvt-production-30fs.tpr -o nvt-production-30fs-c.gro -pbc mol -n index.ndx

Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write gro: Coordinate file in Gromos-87 format
Reading file nvt-production-30fs.tpr, VERSION 2021.2 (single precision)
Reading file nvt-production-30fs.tpr, VERSION 2021.2 (single precision)
Select group for output
Group     0 (         System) has 4242871 elements
Group     1 (          Other) has 3819204 elements
Group     2 (           IAUM) has 18642 elements
Group     3 (              W) has 3798848 elements
Group     4 (            ION) has  1714 elements
Group     5 (        Protein) has 423667 elements
Group     6 (      Protein-H) has 423667 elements
Group     7 (        C-alpha) has     0 elements
Group     8 (       Backbone) has     0 elements
Group     9 (      MainChain) has     0 elements
Group    10 (   MainChain+Cb) has     0 elements
Group    11 (    MainChain+H) has     0 elements
Group    12 (      SideChain) has 423667 elements
Group    13 (    SideChain-H) has 423667 elements
Group    14 (    Prot-Masses) has 423667 elements
Group    15 (    non-Protein) has 3819204 elements
Group    16 (          W_ION) has 3800562 elements
Group    17 (       IONs_all) has  1714 elements
Group    18 (   IAUM-Pro-ion) has 444023 elements
Group    19 ( IAUM-Pro-modif) has 442339 elements
Select a group: 18
Selected 18: 'IAUM-Pro-ion'
Reading frame       0 time    0.000   
Precision of nvt-production-30fs.xtc is 0.01 (nm)

Program:     gmx trjconv, version 2021.2
Source file: src/gromacs/tools/trjconv.cpp (line 921)

Fatal error:
Index[442309] 4241158 is larger than the number of atoms in the
trajectory file (444023). There is a mismatch in the contents
of your -f, -s and/or -n files.

For more information and tips for troubleshooting, please check the GROMACS
website at

The interesting part is that when I make an new group (Group 19 ( IAUM-Pro-modif) has 442339 elements) including some water indices and removing the ions the code creates the gro file.

Is it a bug in the grompp? or am I doing something wrong?


Maybe I have missed it, but did you use the same file to build the index file and to start the simulation?
Thank you

Hi Alessandra @alevilla,
Thanks for your reply.
Yes, I believe did.

Why don’t you create an index file after creating a gro file from xtc? Then you can pass that index file to extract the required items.