> This blog post has been unfinished for two years. So I am posting in the hopes it will spur me to finish it.
The score of a pose reflects how good its interactions are in that static arrangement, a static snapshot. However, given some energy several of these interactions may break and a different conformation is seen. The best way to describe what does 1 kcal/mol mean is that it is the typical strength of a hydrogen bond, but this is rather weak... in fact this is also the average collision energy of water molecules at 37°C, because that is the molar Boltzmann constant times temperature (kBT/NA). (At that point in the explanation is it paramount to resist the urge to explain that kBT coincides with the mean of the Boltzmann distribution describing the energy of collisions as per Maxwell–Boltzmann statistics or else you get that glazed look thermodynamics seems to illicit even in folk that aren't hangover students)
Therefore, hydrogen bonds do come apart and together rather frequently and in some cases these dynamic properties result large scale switching. This cannot really be determined from a static score —even the per residue scores aren't an indication of dynamic properties. So how does one do an MD run in Pyrosetta?
