listRanges does not have a first element with value 0

User discussions
1

GROMACS version: 2024.4
GROMACS modification: No
Hi all,

Has anything changed in the xtc file format from Gromacs 2024.4 to 2025.0? A friend ran a simulation for me using Gromacs 2025.0 and sent me the results. I tried using trjconv from Gromacs 2024.4 to center, rewrap and perform translational and rotational fitting on the 2025.0 production xtc with

gmx trjconv -s prod.tpr -f prod.xtc -o prod_center.xtc -center -pbc mol -ur compact,

but I get the following error:


Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /data/backup_2025_04_10/Wander/USP_Sanca/septinas/02_LCA_plus_septins/02_gromacs/01_from_wander/02_unzipped/MD_Wander
Command line:
  gmx trjconv -s prod.tpr -f prod.xtc -o prod_center.xtc -center -pbc mol -ur compact

Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading file prod.tpr, VERSION 2025.0 (single precision)
Reading file prod.tpr, VERSION 2025.0 (single precision)

-------------------------------------------------------
Program:     gmx trjconv, version 2024.4
Source file: listoflists.h (line 98)
Function:    gmx::ListOfLists< <template-parameter-1-1> >::ListOfLists(std::vector<int>&&, std::vector<T>&&) [with T = int]

Inconsistency in user input:
listRanges does not have a first element with value 0

For more information and tips for troubleshooting, please check the GROMACS
website at https://manual.gromacs.org/current/user-guide/run-time-errors.html
-------------------------------------------------------

Has anyone ever gotten this error?

Best regards,

Marcos Verissimo Alves
Universidade Federal Fluminense
Volta Redonda, Brazil

2

This is an issue with the tpr file format, not xtc. We apparently changed the format without adding a check.

3

Dear Hess,

Thank you for the prompt reply. This means I’d have to install GROMACS 2025.0 to post-process my files, correct?

4

Or generate a new tpr file with 2024.