[gmx-users] Segmentation Fault

[Mark Abraham]

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