[gmx-users] Re: gmx-users Digest, Vol 27, Issue 35

pim schravendijk pimlists at googlemail.com
Wed Jul 12 12:18:31 CEST 2006

On 7/11/06, gmx-users-request at gromacs.org <gmx-users-request at gromacs.org>
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> Message: 6
> Date: Tue, 11 Jul 2006 17:27:46 +0200
> From: Steven Kirk <Steven.Kirk at hv.se>

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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