[AMBER] Water density near the protein suspiciously low

From: I Lőrincz <lorizoli.gmail.com>
Date: Tue, 27 Dec 2016 22:54:53 +0100

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 - 14:00:03 PST
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