[gmx-users] g_msd segmentation fault

Gavin Melaugh gmelaugh01 at qub.ac.uk
Mon Mar 5 13:39:37 CET 2012

Dear All

I have a system of 40 solute molecules in 480 crown ether solvent molecules.
When I ran the msd analysis on the solvent molecules using the following

g_msd_login_d -f traj.trr -s topol.tpr -mol -o 1_12_400K_sol_msd.xvg

I get  a segmentation fault as follows

Select a group: 4                                        
Selected 4: 'SOL'                                        
Split group of 16800 atoms into 480 molecules            
trn version: GMX_trn_file (double precision)             
Reading frame     800 time 40000.000   Segmentation fault

However when I perform the same analysis on the solute molecules it runs
to completion. I  have checked the configuration of the system at frame
800 and everything seems to be fine. I have also analysed the energy and
there seems to be no problem. Has anybody any idea of what might be



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