하지 마 is 하다 + 말다 (choose not to do), and is mostly in an imperative sense, unlike most other words here.
That is, "to not do XX" is "XX(를) 하지 않다", while "XX를 하지 마" is "Don't do XX!". "하지 말다" is similar.
Most of the words you listed are related in meaning but also differ in both meaning and usage.
- 하지 않다(vi): "not do something" in general. The action or event is never even started.
- 가만있다(vi): to stay put. To remain inactive. Means not acting or moving, especially when one is expected to act.
- 가만하다(vi): same as 가만있다, but this is an obscure word only found in literature nowadays.
- 가만두다(vt): to leave someone or something alone.
- 정지하다(vi): to halt. Formal and mostly for vehicles and machines, or sometimes for military personnel.
- 정지시키다(vt): to stop (vt).
- 그치다(vi): to stop. To let up. Used mostly for natural phenomena (rain for example).
- 서다(vi): 1. to halt or stop. 2. to stand. Used both for people and vehicles.
- 세우다(vt): 1. to top (someone, or a thing). 2. to erect, to have someone standing. Causative of 서다.
- 멈추다(vi, vt): stop an ongoing movement, operation, or an action. (used of people and machines)
- 그만하다(vi): stop an action (of people). Not used of vehicles or machines.
- 그만두다(vt): abandon a plan or intention, or quit an ongoing activity like a job, school, etc.