RE: FATAL ERROR: Duplicate bond when going from nvt to npt

From: Radak, Brian K (
Date: Mon Dec 12 2016 - 09:33:46 CST

Can you post the exact error and the relevant settings?

Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
From: [] on behalf of Marlon Sidore []
Sent: Monday, December 12, 2016 4:02 AM
To: NAMD list
Subject: namd-l: FATAL ERROR: Duplicate bond when going from nvt to npt


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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