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?).
Mark
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