# Gmx msd experiences error while reading index file **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools\ **Created:** [March 11, 2023, 11:40pm UTC](https://gromacs.bioexcel.eu/t/gmx-msd-experiences-error-while-reading-index-file/5961 "2023-03-11T23:40:25Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![subhmaha](https://avatars.discourse-cdn.com/v4/letter/s/ac8455/32.png) [@subhmaha](https://gromacs.bioexcel.eu/u/subhmaha)\ **Post date:** [March 11, 2023, 11:40pm UTC](https://gromacs.bioexcel.eu/t/gmx-msd-experiences-error-while-reading-index-file/5961/1 "2023-03-11T23:40:25Z")
GROMACS version: 2020.4 GROMACS modification: No Here post your question I wanted to calculate properties such as end-to-end distance and radius of gyration of a branched polymer. So I created an index file for the polymer making sure the first and last indices constitute the ends of the longest chain. E.g., [mol1] 10 1 2 3 4 5 6 8 9 11 … 42 7 When I tried to use the same index file to calculate msd, I got an error, Calculating diffusion coefficients for molecules. Reading file md\_1.tpr, VERSION 2020.4 (single precision) Reading file md\_1.tpr, VERSION 2020.4 (single precision) Select a group to calculate mean squared displacement for: Group 0 ( mol) has 42 elements There is one group in the index * * * Program: gmx msd, version 2020.4 Source file: src/gromacs/gmxana/gmx\_msd.cpp (line 888) Fatal error: The index group does not consist of whole molecules ## For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors) I noticed the error goes away if I use an index file where the atoms are numbered in order. I wanted to report this issue so that it might be solved in future versions (if already not solved). I do understand that indices of the same molecule should be together in the case the where the group contains multiple molecules. I just do not understand why the indices in the molecule has to ordered in a certain way. Please let me know if I am not considering something. Thank you in advance.