AMBER Archive (2006)

Subject: RE: AMBER: heating system

From: Ross Walker (
Date: Wed Mar 22 2006 - 10:58:12 CST

What you are seeing are probably vacuum bubbles. These will form when you
run a constant volume simulation where the density of your system is
incorrect. Here I suspect you have simply taken the water box created by
Leap and used it for continuous constant volume simulations. The waterbox
leap creates has too low a density due to the need to avoid VDW clashes.
Hence you should ideally heat the system slowly and then run enough
simulation at constant pressure that the denity equilibrates. You can then
either remain at constant pressure or switch back to constant volume.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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> -----Original Message-----
> From: snoze pa []
> Sent: Wednesday, March 22, 2006 08:46
> To:
> Subject: Re: AMBER: heating system
> Dear Ross,
> I used ptrj and found that water box is fixed but still it is not
> uniformaly distributed as be seen in attached png file. in some region
> it is empty and some region it is in good shape. Any help in this will
> be higly appreciated.
> thanks a lot for your time and efforts.
> regards
> snoze

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