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Does it do any damage to run a fixture long term with only half the bulbs in it?
I have a 20g long and 5g together on a modified 55g stand. I added a solid oak top to set the tanks on since they were narrower than the boards made for the 55g to set on and the center board was broken. I want to extend the ends of the stand up to set my 4' fixture on that I was using on the 55g. Eventually I want to setup a nano saltwater tank in the 20g long but for now I'm using both tanks as plant grow out for the 90g and spawning a few of my fish. I don't see a point in buying fixtures I won't use in about a year from now when I change it to saltwater and want more light. Plus I already have the 4' fixture just sitting around because I don't have space for the 55g. The only problem is even with only half the bulbs in the 5g will still get too much light(3/4ths of a 55w bulb will be over it). Can I difuse the light somehow like covering half in the material they put on ceiling fluorescent strips to soften the light? Both tanks are also going to have several floating plants. If it works I could just stick in the other 55w bulb later and have enough light over the 20g for what I want to do with saltwater.

Fixture ballasts are designed to regulate the amount of energy given to a bulb, no matter how many are in there. As long as you don't go over the limit of the ballast, you shouldn't have a problem. I've been running a double 4' fixture with only 1 bulb in it for my reptiles for over a year now, no problems.

You could put a light diffuser on if you'd like too, or even some wax paper between the light and tank will soften it. I used the wax paper for my rainbows when they were new so they'd not be as skittish Just don't burn anything.

I only use one compact flouro in my 10 gal and leave the other side shaded for the apistos. You will be fine, just as Tim says no worries

The Amazon Nut...