A much better written and complete guide to getting started with MD in ECCE+NWChem is found here: http://saccharides.blogspot.tw/2013/06/ecce-md-calculation.html
Rightclick, new, dynamics
Double-click on the new icon
Click on editor
Make sure the number of step is high enough -- I had a lot of off errors when it was 30, or 300. You should also use an equilibration period -- here I didn't.