From: Radak, Brian K (bradak_at_anl.gov)
Date: Mon Dec 12 2016 - 09:33:46 CST
Can you post the exact error and the relevant settings?
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From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Marlon Sidore [marlon.sidore_at_gmail.com]
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 ?
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