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.
Cheers,
Stéphane
--
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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