[AMBER] system breaks during simulation

From: <moitrayee.mbu.iisc.ernet.in>
Date: Sun, 8 Jan 2012 00:50:16 +0530 (IST)

Dear Amber Users,

I was running long simulations on a complex with three components. Around 65 ns,
one of the subunit breaks off from the complex for a while and again reunites.
The rmsd profile is attached. I do not see any shoot ups in energy, temperature,
volume or pressure. Any suggestions as to what might have gone wrong is
appreciated.

Additional info: I am using Amber9, Zaff for Zn co-ordination (the Zn ions seems
to have displaced over the simulation after around 45ns).

Thanks a lot in advance.

Sincere Regards,
Moitrayee
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Received on Sat Jan 07 2012 - 11:30:02 PST
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