[gmx-users] Generate many random configurations

rankinb rankinb at purdue.edu
Fri Mar 7 01:28:37 CET 2014

You are right...it is physically unreasonable for the particles to occupy the
same space.  I will not be running any MD simulations with the
configurations that I am generating.  I will only use the configurations to
determine the coordination number -- the goal is to emulate an ideal gas,
but with a nonspherical solute shape. 

The initial configuration contains the coordinates of the carbon atoms of a
single tert-butanol (TBA) molecule. I would like to add x additional TBA
molecules at random positions, including random orientations.  Maybe the way
I am doing this will not be feasible, because I really need particles to
overlap such that the g(r) = 1 at all distances.  I was trying to generate
these random configurations in a clever way using GROMACS commands, instead
of reinventing the wheel and writing my own program. Do you know of any
available programs that may be of some assistance?  Otherwise, I may end up
writing my own.


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