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Great thoughts, I use running for my personal thinking/reflection time. It really helps focus on problems I am working on or projects I am thinking about. Focusing on those really helps me get in distance because I don't focus on the running.
Same for me. It is not so much a denotational state but a highly focused experience to process and reflect on what has happened that day (or the day before... I am not so much an earlybird...).
To someone who spends probably way too much time listening to dharma talks, reading Zen books, and meditating, it's always a bit jarring to see these paeans to walking and running that describe how this kind of exercise is a great way to just be ... with your thoughts!

Sometimes the experience of running is used to describe zazen. Then the focus is on the state of flow you can get into, which I think mmurph211 is describing here, where actually thoughts too fade out. Just running -- just feet touching the ground and lifting again, intense breathing, wind & rain, the sting of muscle fatigue, getting tired.

I actually think a lot of people misunderstand why they like walking and running. It's not only that you're free to daydream and let thoughts wander freely. It's also a sensuously immersive ritual that dampens the habitual buzzing-like-a-fridge chatter, focuses the mind in real-time, lets you come a bit closer to forgetting yourself.

Agreed. I think running is probably one of the easiest ways to get in that "thought-less" state often associated with formal meditation. Running doesn't put me "with my thoughts" at all...quite the opposite, actually!
Do you systematically reach this state ? Personally I'm having the same "thought-less" state you describe but only when I'm running close to my VO2Max or after a long slow session. But when I run in low speed endurance (70% or less of my heart-rate) thoughts fly through my head.
I think this is true of most endurance sports really. In my own, I wake up well before sunrise every day, bike through the city which is completely deserted and get to watch the sun come up over the water all morning.

It's become something of an addiction as while its stressful on the body, there is nothing that parallels the serenity of being completely alone out in the middle of a perfectly flat lake or river.

Definitely agree. I can't run (bad knees), but there's nothing better than a long, solitary ride. Even in the middle of the city when riding to work, it's easy to zone out and enjoy the solitude.
Highly recommend Harumi Murakami's "What I Talk About When I Talk About Running" if you wish to read more inner thoughts about running.
You don't even need to be in the woods to get to this zen like state he describes when running. I love trail running out in the wilderness, but I find plenty of solitude and peace running in more industrial areas of cities in the early morning hours. Listening to music when running is, for me, counterproductive. The rhythm of the music != to the rhythm I maintain with my breathing. My favorite city runs are on winter mornings when there's a light snow on the ground. It dampens all the noise and everything is quieter.
Early morning is the key. I find running anywhere suburban when there's a chance of traffic, pedestrians, dogs, strollers, crosswalks, lights, etc.. deeply offputting, which is unfortunate when you live in suburbia and it's your only option without driving to a trailhead.
It is reading things like this that make me sad that physiologically I am just unable to run long distances anymore. After some period of time, maybe 20-30 minutes of running, my knees start to become unbearably sore and painful. I've tried everything that I know to. I've modified my stride, new shoes, barefoot running (actually running in vibrams led to one of the most productive fitness periods of my life, including running 6-7 miles a day), and strengthening accessory muscles/connective tissue through weight training. Even at my second-lowest lifetime weight (170ish lbs, second only to my weight right after USMC boot camp of 149lbs) the pain persisted.

Through it all unbearable leg pain caught up with me and stopped me short of truly being able to run as much as I want. The longest I've run was 13 miles and that was only by running until knee pain, then "walking it off" then resuming running, repeating until the end.

I miss running.

One more thing you could try is getting a good foam roller (Trigger Point is the one I have) and rolling out your muscles before and after running.

I use to have problems whenever I upped my mileage but that sorted it out after a few weeks. YMMV but I know it's helped many others too.

Other Anecdote: I have a triggerpoint and I do not think its that great for my muscles and is certainly not going to help out with knee or other joint pain.
This sounds a little obvious but since you omitted it, have you done a gait analysis or seen a physical therapist?

After my first marathon my knee was unbearable, it turns out I cave inwards frequently. The PT gave me daily exercises to correct this and I can now run again.

I have heard great things about the UCSF RunSafe clinic if you are anywhere near there.

You say that you've "tried everything that [you] know" -- does that include seeing a doctor and/or physical therapist? If you haven't, please do: many (most) running injuries are curable with the right training and rehab. A good PT can probably set you on a path back to 6-7 miles per day (and beyond!)

Anecdote time: last winter I started having serious, eventually debilitating knee pain. I went from 30-40 mpw to a point where even a couple miles hurt like hell. I have shitty health insurance and resisted seeing a PT for months, worried about the cost, hoping I could just "tough it out." Yeah, not so much. I finally saw a PT in January, got diagnosed with classic ITBS, and started rehab. Within a month I was back to 3-5 mile runs, and by March I was ready to run a half marathon. I'm keeping up with the strengthening exercises my PT assigned, and the ITBS is just a painful memory.

And the costs I was worried about didn't turn out to be much of an issue: my PT was willing to work with me and my crummy insurance to figure out a way to make it affordable. I only ended up paying about $250 for a couple months of visits — a small price to pay to be able to run again!

See a physical therapist!

Yeah I actually did not do any physical therapy. You're exactly right (I self-diagnosed ITBS myself)..
I run a least six miles every day to force myself away from computers, phones and everything else.

It's calming.

I love running, I'm addicted to it. I got some of my best ideas while I was running. Ideas for apps, ideas for university papers back when I was studying, and much more. For a time, I used to listen to ebooks but that didn't work at all because my mind would always wander off and think about new ideas, so usually after 5min of running I'd completely stopped listening to the ebook voice.

I also prefer music without voice (like minimal house) or with lyrics that are barely existent or not understandable gibberish.

Oftentimes I don't use music at all though, simply enjoying the sounds of nature.

It's a really good diversion to being a single startup founder and hacking all day.

"Sweat cleanses from the inside. It comes from places a shower will never reach." - Dr. George A. Sheehan
Glad to see someone point out running for its calming and therapeutic aspect, instead of the exercise aspect. People always give me strange looks when I tell them I listen to mellow jazz and reggae whilst running, instead of hard and heavy electronic or rock music. Or that I slowly run 10 miles instead of sprint two miles. Running is a time to just "veg out" and let my mind wander. Some of my best ideas and solutions came about from the clarity gained during running.