[gmx-users] Segmentation Fault

[Tsjerk Wassenaar]

Hi George,

And what does the .log tell you? Did grompp give any errors? Did
energy minimization succeed?

Cheers,

Tsjerk

On 4/24/07, George Abadir <georgea at ece.ubc.ca> wrote:
> It says:
> "Starting mdrun 'ICE in water'
> 300000 steps,   45.0 ps
> Back off! I just backed up final traj.trr to ./#finaltraj.trr.20#
> Segmentation Fault"
>
> Thank you,
> George
>
> Mark Abraham wrote:
>
> > George Abadir wrote:
> >
> >> Hi,
> >>     I am doing a simulation of a carbon nanotube in water. I have
> >> done the energy minimization successfully and when I passed to the
> >> molecular dynamics simulation it terminated with "Segmentation
> >> Fault". It seems the only way to bypass this is to reduce the time
> >> step "dt" to 0.1 fs which is very low and thus the simulation takes
> >> very long (actually it has been running for 6 hours now and yet no
> >> more errors anyway). What is the reason of this error? Does anybody
> >> know of a better solution? Is there something to change in the input
> >> parameters or a further step needed that allows the use of a larger
> >> timestep?
> >
> >
> > You'll need to tell us what GROMACS says other than "Segmentation
> > Fault". Segfaults are generic memory errors that can't be traced
> > without more information.
> >
> > Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623