An example with water and TREMOLO

We want to create a box filled with water.

First, we need the following file singleh2o.data:

# ATOMDATA Id name resName resSeq x=3 charge type neighbors=2
# INPUTCONV shift 6.25 6.25 6.25
# INPUTCONV periodic 1
# INPUTCONV temp 0.55
# OUTPUTCONV shift -6.25 -6.25 -6.25
  1  OH2 TIP3  1   1.583   1.785   1.480 -0.8340  OT    2   3
  2  H1  TIP3  1   1.186   1.643   2.213  0.4170  HT    1   0
  3  H2  TIP3  1   2.642   1.896   1.730  0.4170  HT    1   0

Take the remainder of the required files (for a TREMOLO simulation) from the respective h2o example of TREMOLO.

Next, we create a 10x10x10 box filled with water at 1g/cm³ by calling molecuilder as follows:

molecuilder --parse-tremolo-potentials h2o.potentials -i h2o.data -o tremolo xyz --change-box "10,0,10,0,0,10" --fill-void singleh2o.data --distances "3.1,3.1,3.1"

We explain briefly the function of each action:

• --parse-tremolo-potentials: parses a TREMOLO's potentials file. Without it, molecuilder does not know that OT actually refers to an oxygen atom (with element symbol O)
• -i: This is the specification of the output file (also the input file, if it contains atoms already, water is filled around it).
• --change-box: We set the box dimension by giving a vector of each edge's lengths.
• --fill-void: The empty space in the box (i.e. all of it) is filled with the atoms given by singleh2o.data. --distances refers to the distance between each molecule's center per axis (x,y,z). Note that you may also specify --random-atom-displacement, --random-molecule-displacement, and --DoRotate to give the maximum random displacement for each atom, each molecule or a general rotation. Note even more that you can specify the random number generator used by the action --set-random-number-distribution. Thereby, you can even have the random angles for rotation drawn from a discrete set and hence generate a discrete set of orientations of the water molecules.

If you are interested in how the last note works, try this:

molecuilder --parse-tremolo-potentials h2o.potentials -i h2o.data -o tremolo xyz --change-box "10,0,10,0,0,10" --set-random-number-distribution uniform_int --random-number-distribution-parameters "min=0;max=4" --fill-void singleh2o.data --distances "3.1,3.1,3.1" --distance-to-boundary 2 --DoRotate 1

Now, we need some more parameters:

• --set-random-number-distribution: set the random number distribution, here a uniform integral distribution.
• --random-number-distribution-parameters: We set min to 0 and max to 4, i.e. we have a five-sided dice.
• --distance-to-boundary: Minimum distance to boundary should be 2 for the molecule to be placed, otherwise it is removed.
• --DoRotate: Enable random rotations.