Pulling, reversibility velocity

Fig. 8.3. Histogram of work values for Jarzynski s identity applied to the double-well potential, V(x) = x2(x — a)2 + x, with harmonic guide Vpun(x, t) = k(x — vt)2/2, pulled with velocity v. Using skewed momenta, we can alter the work distribution to include more low-work trajectories. Langevin dynamics on Vtot(x(t),t) = V(x(t)) + Upuii(x(t)yt) with JcbT = 1, k = 100, was run with step size At = 0.001, and friction constant 7 = 0.2 (in arbitrary units). We choose v = 4 and a = 4, so that the barrier height is many times feT and the pulling speed far from reversible. Trajectories were run for a duration t = 1000. Work histograms for 10,000 trajectories, for both equilibrium (Maxwell) initial momenta, with zero average and unit variance, and a skewed distribution with zero average and a variance of 16.0...

Allen and Bevan (80) have applied the SMD technique to the study of reversible inhibitors of monoamine oxidase B, and this paper will be used as an example for discussion of the constant velocity SMD pulling method. They used the Gromacs suite of biomolecular simulation programs (18) with the united-atom Gromos 43al force field to parameterize the lipid bilayer, protein, and small-molecule inhibitors. The protein was inserted into their mixed bilayer composed of phosphatidyl choline (POPC) and phosphatidyl ethanolamine (POPE) lipids in a ratio known to be consistent for a mitochondrial membrane. Each inhibitor-bound system studied was preequilibrated in a periodic box of SPC water (20) with the simulations run using the NPT ensemble at 300 K and 1 atm pressure for 20 ns. Full atomic coordinates and velocities were saved in 200-ps increments giving five replicates for each inhibitor-bound system. A dummy atom was attached to an atom (the SMD atom shown in Fig. 7) of the inhibitor nearest to the... 

A schematic diagram of a cyclotron. The ion is introduced in the center and is then pulled back and forth between the hollow D-shaped electrodes by constant reversals of the electric field. Magnets above and below these electrodes produce a spiral path that expands as the particle velocity increases. When the particle has sufficient speed, it exits the accelerator and is directed at the target nucleus. 

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