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Message: 6
Date: Tue, 11 Jul 2006 17:27:46 +0200
From: Steven Kirk <[EMAIL PROTECTED]>
Consider a pair of spherical macromolecules of diameter ~2.5 nm,
arranged along an x-axis so that their centres of mass are 4nm apart,
then centered in a 14 x 10 x 10 nm periodic box,
The box is then filled with TIP4P water, energy minimized, run with
nsteps = 1000000 ; total 1000 ps.
The problem is that when I run this simulation, the expected drift of
the macromolecules towards each other does not occur.
Regards,
Steve Kirk
This is a huge system! How many water molecules do you have? What is the experimental diffusion constant of these particles in water? In any case, in 1 ns you probably won't see much happening there. I guess in 10 / 100 ns you won't see much drift happening as well. Probably you need some form of distance dependent free-energy ( e.g. distance constaints) method to get any wiser about the drift of the molecule
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