Using the XML native format defined in GAMGI (GML), a water molecule can be written as:

    <atom element="O" x= "0.000"  y="-0.0679" z="0.0000" id="O1"/>
    <atom element="H" x= "0.7754" y= "0.5392" z="0.0000" id="H1"/>
    <atom element="H" x="-0.7754" y= "0.5392" z="0.0000" id="H2"/>

    <bond parent1="O1" parent2="H1"/>
    <bond parent1="O1" parent2="H2"/>
The file $GAMGI/dat/gamgi/all.xml is a fully working example, containing all the parameters that GAMGI accepts, for both object and configuration data. Using the xyz standard format, the same water molecule can be written as (in this case the bonds must be added afterwards):

This is a comment line
  O          0.0000         -0.0679          0.0000
  H          0.7754          0.5392          0.0000
  H         -0.7754          0.5392          0.0000
In both formats, white lines and spaces are discarded.