Molecular dynamics simulations bonded interactions

Ligand-Protein Interactions The energy of formation of ligand-protein contacts can be computed as a sum of non-bonded (Lennard-Jones and electrostatic) terms similar to those used in a molecular dynamics simulation. 

Parallel molecular dynamics codes are distinguished by their methods of dividing the force evaluation workload among the processors (or nodes). The force evaluation is naturally divided into bonded terms, approximating the effects of covalent bonds and involving up to four nearby atoms, and pairwise nonbonded terms, which account for the electrostatic, dispersive, and electronic repulsion interactions between atoms that are not covalently bonded. The nonbonded forces involve interactions between all pairs of particles in the system and hence require time proportional to the square of the number of atoms. Even when neglected outside of a cutoff, nonbonded force evaluations represent the vast majority of work involved in a molecular dynamics simulation. 

Example If a drug molecule interacts with a receptor molecule through hydrogen bonds, then yon might restrain the distance between the donor and acceptor atoms involved in the hydrogen bonds. During a molecular dynamics simulation, these atoms would slay near an ideal value, while the rest of the molecular system fully relaxes. 

Medium-range interactions can be defined as those which dominate the dynamics when atoms interact with energies within a few eV of their molecular binding energies. These forces determine a majority of the physical and chemical properties of surface reactions which are of interest, and so their incorporation in computer simulations can be very important. Unfortunately, they are usually many-body in nature, and can require complicated functional forms to be adequately represented. This means that severe approximations are often required when one is interested in performing molecular dynamics simulations. Recently, several potentials have been semi-empirically developed which have proven to be sufficiently simple to be useful in computer simulations while still capturing the essentials of chemical bonding. 

Far IR spectroscopy is a useful technique to study the structural environment and dynamics of water molecules and ions in the interlayer galleries of LDHs, since it directly probes the intermolecular and hydrogen bonding interactions [223]. Spectra, which can be recorded by pressing small amounts of powder onto one side of a piece of Scotch tape, are often difficult to interpret because of the complex network of intermolecular interactions present and molecular dynamics simulations have been employed in order to assist in the interpretation [223]. 

We now present results from molecular dynamics simulations in which all the chain monomers are coupled to a heat bath. The chains interact via the repiflsive portion of a shifted Lennard-Jones potential with a Lennard-Jones diameter a, which corresponds to a good solvent situation. For the bond potential between adjacent polymer segments we take a FENE (nonhnear bond) potential which gives an average nearest-neighbor monomer-monomer separation of typically a 0.97cr. In the simulation box with a volume LxL kLz there are 50 (if not stated otherwise) chains each of which consists of N -i-1... 

---