Dan Ensign @ Stanford wrote:Okay, here it is: The CLONE numbers are labels for each trajectory that we run. Each GENeration is another chunk of time along that trajectory. So, say that I benchmark CLONE0, GEN0 (the first 4 ns). That WU is then done, and the FAH software builds a new WU with starting coordinates (and velocities and stuff) where mine left off. Then the new WU -- GEN1 of CLONE0 -- gets sent to you, and you simulate the next 4 ns. And so on. So CLONE is a label for an individual trajectory, and GENerations are time steps along that trajectory.
RUNs are groups of similar CLONEs. All the CLONEs in a RUN have the exact same atoms, the exact atom positions, the same temperature, etc. The difference is the starting velocities -- the initial motions of all the atoms in the protein are randomized. Although statistically the velocities are determined by the temperature, there are countless ways of partitioning the velocities to the atoms, so we try out 100 or so CLONEs to get a good feel for the sample space. Assigning different velocity sets to the atoms turns out to be wildly important: if the conformation we start with happens to represent the transition state (sort of halfway from folded, halfway from unfolded) then 50 of our 100 CLONEs will fold, and 50 won't.
The different RUNs in a PROJect might, in their simplest form, represent different starting conformations. So, we could start off 100 RUNs of different partially unfolded structures and try to find the one for which half of its CLONEs fold -- then that RUN has the conformation of a representative of the transition state.
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