[gmx-users] Generate many random configurations

[Justin Lemkul]

On 3/6/14, 7:27 PM, rankinb wrote:
> 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.
>

So you basically need infinite sampling via some finite number of 
configurations.  I doubt you'll get that with genbox.  If you require g(r) = 1 
for all positions, that's just a regular grid with atoms occupying every point 
at which the RDF is measured (every 0.002 nm in g_rdf, by default).  I suppose 
one could try to generate enough random configurations that are different but do 
not enrich any particular site, but that sounds like a losing battle to me.  So, 
in short, no, I can't think of a particularly clever or Gromacs-centric way to 
do this.  Maybe someone else can, but it looks like you're trying to make genbox 
do something it's not likely to accomplish.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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