[gmx-users] Segmentation fault 3

[Christoph Freudenberger]

Tanos C. C. França wrote:
>  
> 
>  
> 
>             Hi folks,
> 
>             I am facing the problem of segmentation fault again 
> !!!!!!!!!!!! This time I am trying to perform a Position Restrained (PR) 
> molecular dynamics (MD) of a crystallographic structure I have used 
> before to build a model by homology. I used the same parameters as to 
> the model but the calculation did not go on. With the model everything 
> went fine. I have performed 10 ps of PR MD and latter 100 ps of MD but 
> with the crystal structure nothing seems to work !!!!!!!!!!!!! I am 
> sending below the tail of my prlog.log file and my pr.mdp file.

You're using
constraints         =  all-bonds
with the default LINCS algorithm. Looks like your system gives coupled
constraints that cannot be resolved by LINCS (check the manual about that).
Try using
constraints         =  h-bonds
or
constraints         =  none
or if you really need all bonds constrained:
constraint-algorithm =  shake
-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785