[gmx-users] Segmentation fault after dt=2fs

Stéphane Téletchéa steletch at jouy.inra.fr
Mon Jul 16 15:37:22 CEST 2007

Mahnam a écrit :
> In God We Trust
> Hello Dear Dr David van der Spoel
> Thank you for your quick response. I  had used constraints before md 
> simulation. 
> I have done energy minimization and position restraint (20ps) (with 
> constraints=all bonds )and then md simulation at 100 K, 200K and 300K for 
> 100ps (with constraint=none) and then I extended my simulation at 300K for 
> 700ps (e.g. 1000ps md simulation)  with time step 1fs and everything is ok, 
> only if I change time step to 2fs, it crashes.

In order to use 2 ps time steps, you need to constrain the h-bonded 
interactions, using "h-bonds" instead of none should solve you problem.

Consider also coupling counter-ions and solvent as mentionned by Justin 
A. Lemkul.


Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

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