all you have to do is call force.start which runs through the declared nodes again and changes the charges and other properties on them.
svg.on("click", function() {
force = force.charge(function(d, i) { return i ? 0 : -50000; })
force.start()
window.setTimeout(function() {
force = force.charge(function(d, i) { return i ? 0 : -2000; })
force.start()
},3000);
});