They're adjusting the integration method (used to calculate positions given forces) to take into account the properties of the thermostat (used to maintain a roughly-constant temperature in the simulation). This allows bigger timesteps.
In particular, they studied the Langevin thermostat, in which all the atoms are subject to small random forces that smooth out their average temperature. By adding a term to the integrator that includes the magnitude of the random forces, it is possible to widen the stability bounds of the integration.
The caveat is that the proof is only for simple potential energy surfaces. They haven't given a lot of evidence, even empirically, that this works for the potential energy surfaces we really care about, like protein binding calculations. We already have many empirical tricks for increasing timesteps for these simulations, like freezing bond lengths for hydrogen. Any new method has to beat these empirical methods, not just beat a naive approach.
Yeah I've worked a lot with this and was also curious as the thermo distribution is just one part, you also have a lot of short range forces that explode if you increase the timestep by too much and I didn't see any tricks around that (except the usual like freezing the fastest degrees of freedom, completely removing hydrogens with virtual sites etc).
This is a great example of why someone else should write the high level description for somebody else's work. Without the baggage of what was hard, fun, easy, interesting (and the desire to sell/market), an outsider can focus on the importance and utility of a work.
Thanks for the feedback. I'm still trying to flesh out the concept. This post was an attempt to do that via examples, but I guess I haven't really succeeded.
Was it the structure you found unclear? Or the examples/analysis?
> it's not actually true that they're less dependent on the state than "city folk." Hell, in many cases rural areas are more dependent on the state.
I'd like to see you back up this claim, but either way dependence on "the state" isn't really what matters.
What matters is the interdependence between the two locales. Cities are almost entirely dependent on rural areas for their food. Rural areas could continue to exist without cities; the reverse is not true.
Cities are also more fragile than rural areas. Say something catastrophic were to happen to some region of the US, something that wiped out communications infrastructure, electricity generation, supply routes (roads, rail), etc. The cities in this region would be foodless within a few days. Depending on the city, there would be either no running water or dirty running water. Even if martial law were quickly instituted, violence and starvation would result.
Contrast this to the rural areas. Food would certainly be an issue, but it is more likely that the population is either (a) near agricultural infrastructure or (b) prepared to fish/hunt/forage. It helps that there are less mouths to feed.
Furthermore, most people are on wells and/or septic tanks, which barring damage gives them a much longer timeline before water/sanitation becomes an issue. Again, it helps that there is a lower density of people needing drinking water and sanitation.
I guess my ultimate point is that strategically, it is the rural areas holding the cards. Would they be poorer without the cities? Absolutely. Could they survive? They did for generations.
There are very few rural areas in the US in which most people don't get their food from the supermarket, water from utilities and power from a power company, just like everyone in a city. They didn't build their homes from trees they felled by hand, they don't grow their own food, or sew their own clothes.
As far as hunting and fishing goes, few people living in rural areas would be capable of living entirely off the land for an extended period of time, so the premise that they would be able to survive a disaster more or less unscathed while the city dwellers starve is just really not true, at least not as true as Americans would like to believe.
One problem rural areas do have is lack of disaster preparedness funds. I live in Texas, and I've seen what happens when disasters hit rural areas. The same people who complain about Washington and city dwellers wind up in tent cities being tended to by the Red Cross and FEMA.
See how well agricultural communities do without farm subsidies, housing loans or food stamps. Without the state keeping them alive, a lot of them would simply die out.
And this is my ultimate point - most Americans who live in rural areas are little less domesticated than their urban counterparts.
