RE: AMBER: Does amber use water density around 1 at room temperature

From: Ross Walker <>
Date: Tue, 23 Jan 2007 15:11:41 -0800

Dear Li,

> Sorry to bother. I am just wondering whether amber is using
> water which has
> density around 1 g/mm^3 when using leap to solvate by the command
> solvatebox. Because I was trying to construct a box of pure water by
> solvatebox of an empty unit. When setting boxside to be 34 or
> so, I get 853
> water in it, which makes the density less than 0.7. Is it
> normal? If so.
> Then, is tryint to contral the pressure will be the way for
> me to get the
> density to be around 1? Thank you very much in advance!

What you are seeing is a function of the approach by which leap actually solvates a molecule. The various water boxes, TIP3PBOX etc have been equilibrated to have approximately 1g/cm3. Now when you come to solvate your system leap teselates these boxes and removes any waters that have close contacts to your protein. At the same time it removes waters around the edge of the box that might have steric clashes with the images. This is where the 0.7g/cm3 comes from. In order to avoid potentially simulation destroying VDW clashes between waters leap removes more waters than would strictly be necessary.

However, the problem is easily fixed. Firstly you want to run a minimization followed by about 50ps or so of MD at constant volume where you heat up from 0K to around 100K or so. You shouldn't run much longer than 50ps here because otherwise you will start to get vacuum bubbles that can take a very long time to equilibrate out. The reason you can't just start with constant pressure is because the calculation of pressure is very inaccurate a low temperatures. You can then run a couple of hundred ps or so of constant pressure heating up to 300K or whatever temperature you need. You can watch the pressure as a function of time, along with the box size / volume / density to determine when the system has equilibrated. At this point you should have a reasonable density. It won't be exactly 1g/cm3 because of the presence of your solute. Once the density has equilibrated you can, if you want, switch back to a constant volume simulation.

I hope this helps,

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Wed Jan 24 2007 - 06:07:44 PST
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