[gmx-users] Long range forces, periodic boundaries and aggregation

Mark Abraham Mark.Abraham at anu.edu.au
Tue Sep 27 16:34:58 CEST 2005

Steven Kirk wrote:
> Hello,
> Firstly, many thanks to David and the others who answer users questions on this list. Your help has been invaluable to me in the past.
> I have a large, approximately spherical macromolecule (silica nanoparticle, approx. 4 nm in diameter) which I am investigating in TIP4P water. I put the molecule centered in a cubic box of side 6 nm, then build another cell which is effectively two of these boxes side by side in the X-direction. The resulting simulation cell is then 12x6x6 nm, and I then add TIP4P water using genbox. I am using PME electrostatics, with a FFT grid spacing of 0.12 nm, a pme_order of 6, a time step of 0.001 ps and a simulation run time of 80 ps. 

I assume your system is, in fact, periodic.

If your system is periodic, the "left" nanoparticle has a "right" 
nanoparticle on the right, _and_ on the left. By your construction both 
of these "right" nanoparticles are equidistant from the "left" 
nanoparticle. If the nanoparticles are attractive, this state should be 
metastable in the long-axis direction - eventually thermal motion will 
kick a particle one way far enough to get them into the energy well.

The up and down motion could be suggestive of repulsive nanoparticles. 
They are keeping the same distance to the periodic copies in the 
short-box-side directions and increasing the distance to the copies in 
the long-box-side directions.

This is almost certainly not what I think you were intending to study, 
which is two particles in isolated solvent. Your solvation shell will 
need to be significantly larger than your interparticle distance range 
of interest to model this adequately.

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