[gmx-users] Segmentation fault 2

[Christoph Freudenberger]

Hi Tanos,

Tanos C. C. França wrote:
> Dear Christoph,
> 
>  
> 
> Before md, I’ve performed an energy minimization in my system until 1000 
> Kj/mol.nm and, than, a pr dynamics of 10 ps with all bonds constrained. 
> This two steps were successful.  
> 
> Following your suggestion I’m going to try to perform the dynamics with 
> no constraints.
Sorry if this wasn't clear from my previous mail.
If the system as been running stable already in the minimization and the
10 ps MD WITH constraints it does no make sense to turn them off again now.
Check what changed from 10ps.mdp (the one that went well) to 50ps.mdp
(the one that crashes).

As a first guess I would reduce the timestep to 0.001ps, tau_p = 0.5 is maybe
also a little bit hard for an unequilibrated system, although you don't get
any pressure scaling warnings. try tau_p = 2 or 5.

regards
-- 
Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785