[gmx-users] g_msd segmentation fault

Mark Abraham Mark.Abraham at anu.edu.au
Mon Mar 5 13:56:49 CET 2012

On 5/03/2012 11:39 PM, Gavin Melaugh wrote:
> 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
> comand.
> 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
> happening?

Running out of memory would be the first suggestion. A segmentation 
fault is a generic error message when a C program (ie. GROMACS) has 
assumed that it can get access to a certain amount of memory, but is in 
fact doing so in a way that breaks the rules that "segment" memory so 
that one (part of a) program can't hurt another one.

Running in single precision will roughly halve your memory requirements, 
probably without affecting your results. Reducing the number of frames 
can help also, but it seems you already have fairly few frames. Using 
-mol probably increases the amount of memory you need by an amount 
proportional to the number of such molecules (or maybe its square?).


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