Re: [AMBER] Water density near the protein suspiciously low

From: Chris Moth <>
Date: Tue, 27 Dec 2016 16:42:07 -0600

Is there any chance this is a long simulation, and the "missing waters"
have wandered into other periodic cells - and you not wrapped them back
into the main cell for analysis?

Are the dimensions of the simulation cell also changing dramatically
between AMBER and GROMACS?

On 12/27/2016 3:54 PM, I Lőrincz wrote:
> Hello everyone,
> I've been constant pressure (1 bar) simulations with both AMBER 11 and
> GROMACS. At the end of the simulation water is much more densely packed
> near the protein when using GROMACS, then AMBER.
> For example, at the end of a simulation with GROMACS I found 4232 water
> molecules within a 5 Angstrom radius of my protein, whereas running a
> simulation with the same parameters with AMBER I only found 3054 water
> molecules within 5 Angstroms of the same protein (72.2% of the waters in
> GROMACS). Moreover, there were 2528 water molecules within a 3 Angstrom
> radius of the protein after the GROMACS simulation, but only 1570 water
> molecules after the AMBER simulation (62.1% of the GROMACS waters).
> What could be the reason for the difference and why does AMBER - apparently
> - cause a local decrease in water density close to the protein?
> Any advice, comment or explanation on this would be much appreciated.
> István Lőrincz
> Department of Biochemistry,
> Eötvös Lorand University, Hungary
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Received on Tue Dec 27 2016 - 15:00:02 PST
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