I do not think that running twice a week will be that awful, you will still be able to put muscle on. Just make sure it is not hurting your recovery too bad, and keep note of all your lifts, and if your lifts are progressing you will gain muscle.
Do what you want to do, if you like to run, do it. When I was in my freshman year of college I used to do long distance running 3-4 times a week and I still put on a lot of muscle. Just make sure you eat enough so your body can add muscle