[gmx-users] Error: GROMACS GMX HLEIX segmentation Fault

[Budheswar Dehury]

Dear Gromacs Develeopment Team,


Hello...I have the same segmentation fault of gmx helix even after updating with the revised version and/or applying the patch for the same. further I have alos tried to compile using the source-code of the latest version, I am facing the same segmentation fault problem.


Here is the command that I executed ..and the error


GROMACS:      gmx helix, version 2019-beta2-dev-20181026-7ce2d66
Executable:   /apps/gromacs/gromacs-2019-git/bin/gmx
Data prefix:  /apps/gromacs/gromacs-2019-git
Working dir:  /run/media/bude//Helix/TM1
Command line:
  gmx helix -s ../md.tpr -f ../md.xtc -n index.ndx

Reading file ../md.tpr, VERSION 2018.2 (single precision)
Reading frame       0 time 200000.000   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 (            TM1) has   397 elements
Select a group: 17
Selected 17: 'TM1'
Checking group TM1
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
t=200000.00Segmentation fault
Need your valuable input to rectify the error.

Thanking You

With Warm Regards

Budheswar