Hi Moitrayee,
On 7/01/2012, at 2:20 PM, moitrayee.mbu.iisc.ernet.in wrote:
> 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).
Are you by any chance wrapping your system into the primary unit cell (iwrap = 1)? If you are, that could easily account for this behaviour as a molecule "jumps" from one side of the periodic cell to the other. Likewise, naïve wrapping commands in ptraj or cpptraj can tear subunits away.
A conventional solution is to (in ptraj or cpptraj) wrap everything around the centre of the first subunit, then around the centre of the combined first and second subunits, then around the centre of the combined first, second and third subunits, and so on, building up your system piece by piece, and saving solvent and counter-ions until the very end. By wrapping this way, you should ensure that your system ends up in the middle of the displayed periodic box.
Good luck,
Ben
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Received on Sat Jan 07 2012 - 11:30:03 PST
