Molecular dynamics chain force

Including solvent in a molecular dynamics simulation creates a frictional force that damps some motion of the solute. This affects in particular the motions of exposed side chain in proteins. 

Concluding this section, one should mention also the method of molecular dynamics (MD) in which one employs again a bead-spring model [33,70,71] of a polymer chain where each monomer is coupled to a heat bath. Monomers which are connected along the backbone of a chain interact via Eq. (8) whereas non-bonded monomers are assumed usually to exert Lennard-Jones forces on each other. Then the time evolution of the system is obtained by integrating numerically the equation of motion for each monomer i... 

For molecular dynamics (MD) simulations to accurately reflect chain motions and conformational changes at various temperatures, the rotational barriers must be correct whether they arise from an explicit dihedral term, vdW interactions, or both. Barriers that are too low will allow disorder to occur at simulated temperatures far below experimental temperatures at which transitions and disorders in PTFE are observed. The validity of the barrier heights, especially the one at trans, obtained from the MOPAC AMI calculations and derived force field parameters above was called into question upon comparison to high level ab initio calculations on perfluorobutane (PFB), perfluoropentane (PFP), and... 

The shortcomings of the force field notwithstanding, these preliminary molecular dynamics simulations indicate that modeling of the chain motions of crystalline fluoropolymers and their interactions is sure to be quite rewarding. Further, the results suggest that with additional refinement of the force field. 

A force field for solid state modeling of fluoropolymers predicted a suitable helical conformation but required further improvement in describing intermole-cular effects. Though victory cannot yet be declared, the derived force fields improve substantially on those previously available. Preliminary molecular dynamics simulations with the interim force field indicate that modeling of PTFE chain behavior can now be done in an all-inclusive manner instead of the piecemeal focus on isolated motions and defects required previously. Further refinement of the force field with a backbone dihedral term capable of reproducing the complex torsional profile of perfluorocarbons has provided a parameterization that promises both qualitative and quantitative modeling of fluoropolymer behavior in the near future. 

PCFF force fields, alternatively with molecular dynamics, in order to identify the global minimum of the energy value). The investigated single chain has a polymerization degree DP=25, similar to the results obtained by synthesis. 

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