A note for MOLDY users


MOLDY uses baricenters and quaternions to define the coordinates of each molecule. Therefore, it is necessary to provide reference geometries for each molecule in the simulation. When building the box with Packmol, you MUST give each molecule in the reference geometry you will use in the simulation. Packmol provides baricenters and quaternions for each molecule in this case.

For example, if you want to build a water box, a MOLDY control file could be (charges and parameters are not important):

title=moldy example
end
water 10
1 9.625597 6.787278 12.673000 1. 0. H
2 9.625597 8.420323 12.673000 1. 0. H
3 10.203012 7.603800 12.673000 18. 0. O
end
generic potential parameters
1 1 0. 0. 2510400.0 0 2552.24 0
end
10.000000 10.000000 10.000000 90 90 90 1 1 1
water 0.107296 0.286338 0.365219 0.078302 0.310120 0.945719 -0.057528
water 0.447343 0.469966 0.621341 -0.642889 0.035654 0.044546 0.763832
water 0.195732 0.381473 0.852377 0.708977 -0.079243 0.020401 0.700469
.
.
.


And so, the molecule provided to packmol should be the following (for example, the water.mdy file):

water 10
1 9.625597 6.787278 12.673000 1. 0. H
2 9.625597 8.420323 12.673000 1. 0. H
3 10.203012 7.603800 12.673000 18. 0. O


Don't put "end" at the end of this file, Packmol will try to read it as an atom.

With the input file for packmol:

#------------------------

tolerance 2.0
filetype moldy
output waterbox.out

structure water.mdy
  number 10
  inside box 0. 0. 0. 10. 10. 10.
end structure

#------------------------


Packmol will create the file waterbox.out with the format

10.000000 10.000000 10.000000 90 90 90 1 1 1
water 0.107296 0.286338 0.365219 0.078302 0.310120 0.945719 -0.057528
water 0.447343 0.469966 0.621341 -0.642889 0.035654 0.044546 0.763832
water 0.195732 0.381473 0.852377 0.708977 -0.079243 0.020401 0.700469
.
.
.


that should be added to the control file of MOLDY.

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We thank Dr. Rafael R. Pappalardo from the Dept. Química Física, Fac. de Química, Univ. de Sevilla, Spain, for his interest and help in the implementation of this option.
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Obs. This option is not extensively tested for the new version of packmol, if you have any trouble using it, please contact us.