Archive from user: Budheswar Dehury Dear GROMACS Development Team, Hello everybody. I am doing analysis of helix properties using GMX helix command in Gromacs 2016.4 as well as in 2018.2. While running the command I have the following issue after executing the following command.. GROMACS: gmx helix, version 2016.4 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /storage/home/local/bude-loc/Desktop/PS2/Seed1/TM1 Command line: gmx helix -f ../md1.xtc -s ../md.tpr -n index.ndx Reading file ../md.tpr, VERSION 2018.2 (single precision) Reading frame 0 time 490000.000 Please select a group containing the entire backbone Group 0 ( System) has 201382 elements Group 1 ( Protein) has 22327 elements Group 2 ( Protein-H) has 11159 elements Group 3 ( C-alpha) has 1414 elements Group 4 ( Backbone) has 4242 elements Group 5 ( MainChain) has 5651 elements Group 6 ( MainChain+Cb) has 6978 elements Group 7 ( MainChain+H) has 6986 elements Group 8 ( SideChain) has 15341 elements Group 9 ( SideChain-H) has 5508 elements Group 10 ( Prot-Masses) has 22327 elements Group 11 ( non-Protein) has 179055 elements Group 12 ( Other) has 179055 elements Group 13 ( POPC) has 40468 elements Group 14 ( TIP3) has 138315 elements Group 15 ( SOD) has 146 elements Group 16 ( CLA) has 126 elements Group 17 ( a\_10635-11031) has 397 elements Select a group: 17 Selected 17: ‘a\_10635-11031’ Checking group a\_10635-11031 There are 25 residues There are 23 complete backbone residues (from 2 to 24) nall=397 Reading file ../md.tpr, VERSION 2018.2 (single precision) helix from: 8 through 23 The same problem also in case of 2018.2 . Though the other helix properties including gmx helixorient and gmx bundle works fine in both the versions… I have attached the last ns trajectory with 10 snapshots for your kind perusal and necessary input. Thanking You With Warm regards Budheswar *(from redmine: issue id 2701, created on 2018-10-17 by gmxdefault, closed on 2018-11-28)* * Changesets: * Revision 76c65770f8d31b0a9194311c5c0384d897fd0bae by Paul Bauer on 2018-10-18T10:21:51Z: ``` Fix segmentation fault in gmx helix Changed the logic in tpxio to only try to access the mtop datastructure if it is actually present. Fixes #2701 Change-Id: I268af10dc125a57758f5f3e79e4b14a25050b3b3 ``` * Revision 93bea6f4ccc34e24c69647e77e560b9100a55831 by Paul Bauer on 2018-11-08T18:22:03Z: ``` Actually fix gmx helix segmentation fault The residue indexing in hxprops was wrong because the residue indices used for residue name lookup were wrong. Added some documentation to clarify what this code does. Fixes #2701 Change-Id: Ie6c002be6ff2139f6af27c7b891a180338ae5b20 ``` * Uploads: * [md.gro](/uploads/a3ccc8b41dc5667cf4e87df4d89645ee/md.gro) GRO * [index.ndx](/uploads/dbf7b486c908720e40aa2cd31de60929/index.ndx) Index * [md.tpr](/uploads/61c483bfe8c21f44455cc68460c16410/md.tpr) TPR * [md1.xtc](/uploads/d67e764d270f96ed6683e0ad32352229/md1.xtc) Trajectory