FATAL ERROR: Duplicate bond when going from nvt to npt

From: Marlon Sidore (marlon.sidore_at_gmail.com)
Date: Mon Dec 12 2016 - 04:02:17 CST


I am currently doing a simulation of a membrane protein. The NVT happened
smoothly, with position restraints on the backbone of the protein.
The error appears when activating the pressure control (while keeping the
position restraints). I don't understand this error though, since it ran
fine in NVT - and starting NPT from the result of the NVT.

Why, if there is indeed a duplicate bond in my topology (though I couldn't
find it), did it run smoothly in NVT ? What did I miss ?


Marlon Sidore

PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille

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