Internal coordinate simulation

You need to specify two parameters the et uilibrium value ofthe internal coordinate and the force constant for the harmonic poten tial, T h e equilibrium restraint value deperi ds on the reason you choosea restraint. If, for example, you would like a particular bond length to remain constant during a simulation, then the equ ilibritirn restrain t value would probably be Lh e initial len gth of the bond. If you wan t to force an internal coordinate to a new value, the equilibrium internal coordinate is the new value. 

For the coordinate system used for optimization, redundant internal coordinates are usually best, followed by a well constructed Z-matrix, then Cartesian coordinates, then a poorly constructed Z-matrix. For simulating multiple molecules, Cartesian coordinates are often best. Most programs that generate a Z-matrix automatically from Cartesian coordinates make a poorly constructed Z-matrix. 

Internal coordinate molecular modeling is an efficient instrument with specific advantages that make it an indispensable complement to other existing approaches. It is best suited for simulation and analysis of large-scale structural transformations in biomacro-mole-cules, and at present ICMD is generally considered the most powerful tool in conforma-... 

A. M. Mathiowetz, A. Jain, N. Karasawa, W. A. Goddard III. Protein simulations using techniques suitable for very large systems the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. CN 8921. Proteins 20 221, 1994. 

As an alternative to modifying the X spacing dynamically as the simulation progresses, we can attempt to define a more elaborate X dependence for the force field that takes into account known sampling issues for the system we are considering. X dependence can be introduced to the potential function in many different reasonable ways. The most common is to linearly scale the parameters that define the potential function with X. So, for example, force constants, equilibrium internal coordinates and non-bonded parameters are defined as60... 

In practice, MC simulations are primarily applied to collections of molecules (e.g., molecular liquids and solutions). The perturbing step involves the choice of a single molecule, which is randomly translated and rotated in a Cartesian reference frame. If the molecule is flexible, its internal geometry is also randomly perturbed, typically in internal coordinates. The ranges on these various perturbations are adjusted such that 20-50% of attempted moves are accepted. Several million individual points are accumulated, as described in more detail in Section 3.6.4. 

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