[gmx-users] Generate many random configurations

Justin Lemkul jalemkul at vt.edu
Thu Mar 6 22:46:19 CET 2014

On 3/6/14, 3:05 PM, rankinb wrote:
> I am generating x number of random configurations by iteratively calling the
> genbox command (implemented with a bash script), concatenating the results
> to obtain multiple random configurations, and calculating the g(r) over all
> configurations.  So in a sense, I am calculating the g(r) over a trajectory,
> but the trajectory was not obtained from a simulation.   Here is the bash
> script that I am using to do that:
> #! /bin/bash
> #define number of molecules to add
> nmolecules=1
> #define box length
> boxl=1.50356
> for i in {1..10000}
> 	do
> 		rn=$i
> 		genbox -cp coordinates_i.gro -nmol $nmolecules -ci coordinates_i.gro -box
> $boxl $boxl $boxl -vdwd 0.01 -seed $rn -o coordinates_out$i.gro
> done
> cat tba*.gro >> all.gro
> As I said before, I would like to set vdwd to zero but am receiving an
> error.

Do you know that any of your particles are actually that close?  What is the 
input configuration to which you are adding your molecules?  You mentioned 
something before about an ideal gas, so are you just trying to add random 
particles throughout some void space?  I'll admit that I don't understand why 
anyone would want their particles to be on top of one another, that just sounds 
like a recipe for an unphysical disaster :)  Perhaps you can explain a bit more 
thoroughly what you're trying to do.  Keep in mind that the use of -vdwd does 
not guarantee that any particles will necessarily come very close, it just makes 
it more likely.  The neighbor searching algorithm crashes with "-vdwd 0," so you 
will not be able to do that.



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


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