What does 있는 것 mean?
I understand what 있는 것 means when 고 is added in front of 있는 것 as it makes the verb present progressive. However, what does 있는 것 mean, for example, "함께 있는 것만으로 눈물이 나는 걸요?" Is it modifying something or is this an expression? Thank you.

Question

What does 있는 것 mean?
I understand what  있는 것 means when 고 is added in front of  있는 것 as it makes the verb present progressive. However, what does  있는 것 mean, for example, "함께  있는 것만으로 눈물이 나는 걸요?" Is it modifying something or is this an expression? Thank you.

Answer

"있는 것"

있는 is a present tense conjugation of 있다, which means "to be/stay somewhere".(To exist is its another meaning). 
It is similar to the present participle in English, like "staying", describing an ongoing action or state.

것 is an abstract noun here for an "act" or "fact", so 있는 것 means "the act of being/staying".

For example:
1. 책을 읽고 있다 = (I) am reading a book. 
2. 책을 읽고 있는 것 = to be reading a book. (noun phrase of #1)

있다 and 있는 have many other usages besides -고 있다.

- 길 건너에 은행이 있다 = There is/exists a bank on the other side of the street.

- 집앞에 한 남자가 서 있다 = A man is standing in front of the house.
- 집앞에 서 있는 남자는 아빠 친구였다 = The man standing in front of the house was a friend of my father's.
- 나 오후엔 집이 있을 거야 = I will be home in the afternoon.

(your example)
- 두 사람이 함께 있다 = The two are together. 
- (두 사람이) 함께 있는 것 = (The two) being together.  (noun phrase)
- 함께 있는 것만으로 = just for/by being together. (-만 = only, just; -으로 = for, by (reason or means))
- 함께 있는 것만으로 눈물이 나요 = I tear up just for/by being together (with you).

Answer

https://www.youtube.com/watch?v=aA_UxgRiQTM&lc=z130vlcwzlfixzaih04cgziynrafxx5yvyg0k.1492040550416829

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