Molecular dynamics energy

Molecular mechanics and electrostatics calculations have both played an important role in studying electron transfer proteins. Molecular mechanics calculations of these proteins use the same techniques (molecular dynamics, energy minimization) as for other proteins, although special consideration must be made in simulation conditions. 

In a recent work, Grossman and Mitas have proposed a strategy to correct ab-initio Molecular Dynamics energies with QMC [62]. This is however different from CEIMC because the nuclear degrees of freedom are still sampled on the basis of DFT forces. Therefore, when applied to metallic hydrogen, that method would have found the same liquid structure as obtained by CPMD-LDA [54]. 

We have already discussed in Section 9.5.1 the type of information that NMR experiments can provide about the conformation of a molecule and the use of distance geometry for determining structures that are consistent with the experimental data. In the simplest molecular dynamics approach, we could incorporate harmonic restraint terms of the form k(d - dg) where d is the distance between the atoms in the current conformation and dg is the desired distance dynamics approach derived from the NMR spectrum, k is a force constant, the value of which determines how tightly the restraint should be applied. The information provided by the COSY experiment can also be expressed as a torsion angle via the Karplus equation torsional restraints may be incorporated into the molecular dynamics energy function as an alternative to the use of distances. There are many other ways in which the restraints can be incorporated for example, some practitioners prefer to penalise a structure only if the distance exceeds the target ... 

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