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.
Thanks,
Blake
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