Molecular dynamics simulations sampling programs

All simulations were carried out with the GROM ACS molecular dynamics simulation program [23] with some modification to perform the umbrella sampling... 

Typical molecular dynamics simulation requires a few initial steps this is illustrated in Figure 4-4. Often each of these steps is realized as a separate run of the MD program. First of all, the wave function must be fully converged for the initial configuration of nuclei. If the simulation is supposed to sample the vicinity of... 

In the first step of stage 1, all atoms (5000-25000 atoms for a typical application to an enzyme-catalyzed reaction) are treated on the same footing. In this step, one calculates a one-dimensional potential of mean force (PMF) as a function of the distinguished reaction coordinate 2 by a classical molecular dynamics simulation. Any method for calculating classical mechanical PMFs could be used for example, one can use the CHARMM program to carry out this step by employing molecular dynamics simulation with umbrella sampling. As discussed below, this provides an approximation to the free... 

On-the-fly molecular dynamics have been employed in order to simulate the photochemistry of carbonyl-containing compounds. The on-the-fly mechanism implemented in the MNDO program is the velocity-Verlet algorithm. Here an additional aspect of the usage of a computational cheap semiempirical method is visible. In order to provide realistic relative yields of different photochemical reactions, a large enough sample of trajectories is needed. For these systems, a substantial amount of trajectories (around 100) has been calculated for a relatively long timescale (up to 100 ps). 

As conformational sampling is the main bottleneck in the simulation process, efforts have been made to parallelize AMBER for use in both molecular dynamics and free energy calculations. A recent collaboration involving, in addition to AMBER authors, Mike Crowley of the Pittsburgh Supercomputer Center, has led to a very exciting parallel version of the program which enables each nanosecond simulation of a 40000 atom system, the thyroid hormone receptor, using PME electrostatics to be completed on 128 processor of the CRAY T3E in about half a week, about six times faster than the calculation would have taken on the previous version of the software, which was quite efficient on the CRAY T3D. 

---