# Indexing issue and grompp **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters, grompp, analysis-tools\ **Created:** [October 18, 2021, 5:07pm UTC](https://gromacs.bioexcel.eu/t/indexing-issue-and-grompp/2982 "2021-10-18T17:07:17Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Mohammad](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mohammad](https://gromacs.bioexcel.eu/u/Mohammad)\ **Post date:** [October 18, 2021, 5:07pm UTC](https://gromacs.bioexcel.eu/t/indexing-issue-and-grompp/2982/1 "2021-10-18T17:07:17Z")
GROMACS version: 2021.2 GROMACS modification: No Here post your question I have indexing issue in the xtc file format. my topol.to top file has the following items: ```auto ; 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: ```auto 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. ```auto 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 (-: GROMACS is written by: Andrey Alekseenko Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Gilles Gouaillardet Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. 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 http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- ``` 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? Best, Mohammad ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [October 27, 2021, 10:13am UTC](https://gromacs.bioexcel.eu/t/indexing-issue-and-grompp/2982/2 "2021-10-27T10:13:50Z")
Hi, Maybe I have missed it, but did you use the same file to build the index file and to start the simulation? Thank you Alessandra ---
**Author:** ![Mohammad](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mohammad](https://gromacs.bioexcel.eu/u/Mohammad)\ **Post date:** [October 27, 2021, 2:21pm UTC](https://gromacs.bioexcel.eu/t/indexing-issue-and-grompp/2982/3 "2021-10-27T14:21:05Z")
Hi Alessandra @alevilla, Thanks for your reply. Yes, I believe did. Best, Mohammad ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [October 27, 2021, 4:54pm UTC](https://gromacs.bioexcel.eu/t/indexing-issue-and-grompp/2982/4 "2021-10-27T16:54:09Z")
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.