All-atom molecular dynamics simulations

Wong, K.Y. and Pettitt, B.M. A study of DNA tethered to surface by an all-atom molecular dynamics simulation. Theoretical Chemistry Accounts, 2001,106 (3), p. 233-235. 

Seelig A and J Seelig 1974 The Dynamics Structure of Fatty Acyl Chains in a Phospholipid Bilayer Measured by Deuterium Magnetic Resonance Biochemistry 13-4839-4845 Stouch T R 1993 Lipid Membrane Structure and Dynamics Studied by All-atom Molecular Dynamics Simulations of Hydrated Phospholipid Bilayers. Molecular Simulation 10-335-362. 

Stauch T (1993) Lipid membrane structure and dynamics studied by all-atom molecular dynamics simulations of hydrated phospholipid bilayers. Mol Simul 10 335... 

Fig. 1.3 Image of the HIV-1 virus capsid assembly, revealing the detailed structure obtained via all-atom molecular dynamics simulation [399], This molecule consists of about 1,300 proteins. Left full molecule right close up showing detail of hexamer/pentamer structure. This image courtesy of Juan Perilla and the Theoretical and Computational Biophysics Group at the University of Illinois Beckman Institute...

The most straightforward means of simulating network behavior at the atomic level is molecular dynamics. However, simulations of network stmcture and behavior require the use of large number chains and junctions, and length and time scales beyond the capabilities of present-day computers are needed. For this reason, all-atom molecular dynamics simulations of networks comprising a large number of chains and junctions have not been possible, and different levels of approximations have been adopted. Here, we present some examples of simulations of different features of networks at different levels of approximation. 

All analyses have been performed under classical conditions in order to investigate the entire conformational space over 1 ns, which seems enough to give a reliable result. Indeed, unlike for proteins, a one-nanosecond all-atom Molecular Dynamics simulation is sufficient to achieve convergence of sampling for small systems. A previous study has shown that 1 ns simulations are sufficient to fully sample the conformational space of simple furanoses. The system studied here is sufficiently small that nanosecond timescale simulations are feasible within classical mechanics, but not within the CPMD quantum methodology in the case where solvent has to be represented explicitly. For this reason, only classical results are presented here. 

M. C. Zwier and L. T. Chong, Curr. Opin. Pharmacol., 10,745 (2010). Reaching Biological Timescales with All-Atom Molecular Dynamics Simulations. 

H. Lei and Y. Duan,/. Phys. Chem. B, 111, 5458 (2007). Ab Initio Folding of Albumin Binding Domain from All-Atom Molecular Dynamics Simulation. 

E. Paci, C. Friel, K. Lindorff-Larsen, S. Radford, M. Karplus, and M. Vendruscolo, Pro-ferns Struct., Funct., Bioinf, 54, 513 (2004). Comparison of the Transition State Ensembles for Folding of Im7 and Im9 Determined using All-Atom Molecular Dynamics Simulations with O Value Restraints. 

Further results of all-atom molecular dynamics simulations have also been reported for PEO/PMMA blends [214], POSS/PE blends [215], blends of hydroxyl-terminated polybutadiene with explosive plasticizers [217], as well as a novel force field for PDMS and mixtures with alkanes [216]. The simulation of multiphase polymer systems has also been reviewed [208]. 

One of the major objectives of the physical chemistry studies in water and biomolecules is to fully reproduce the experimentally observed folding/ unfolding behavior of a typical model protein in water by means of molecular simulation. However, the all-atom molecular dynamics (MD) simulation of the folding of a protein from the fully unfolded state to the native structure remains computationally intractable when the size of the target protein is larger than 100 residues and when simulation is carried out with explicit water molecules (i.e., when complete, contextualized simulation is attempted) [1-3]. 

Molecular simulations of ionomer systems that employ classical force fields to describe interactions between atomic and molecular species are more flexible in terms of system size and simulation time but they must fulfill a number of other requirements they should account for sufficient details of the chemical ionomer architecture and accurately represent molecular interactions. Moreover, they should be consistent with basic polymer properties like persistence length, aggregation or phase separation behavior, ion distributions around fibrils or bundles of hydrophobic backbones, polymer elastic properties, and microscopic swelling. They should provide insights on transport properties at relevant time and length scales. Classical all-atom molecular dynamics methods are routinely applied to model equilibrium fluctuations in biological systems and condensed matter on length scales of tens of nanometers and timescales of 100 ns. 

The recent years are characterized by a significant improvement in theoretical methods used in studies of the structures and dynamics of nucleic acids. The most impressive development we have evidenced was the advance of nanosecond MD simulations. Currently, all-atom molecular dynamics techniques for the first time provide stable trajectories of hydrated oligonucleotides on a nanosecond scale without using any constraints. The old MD studies were limited to very short time intervals. When longer simulations... 

Although these studies provided insight, in each case information about some aspect of the bilayer was missing. It seemed clear that an understanding of all relevant structural and dynamical aspects of permeation phenomena required yet more detail. For this reason, despite the computational cost, atomic-level (or united atom) molecular dynamics simulations have been applied to this problem. 

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. 

The first molecular dynamics simulations of a lipid bilayer which used an explicit representation of all the molecules was performed by van der Ploeg and Berendsen in 1982 [van dei Ploeg and Berendsen 1982]. Their simulation contained 32 decanoate molecules arranged in two layers of sixteen molecules each. Periodic boundary conditions were employed and a xmited atom force potential was used to model the interactions. The head groups were restrained using a harmonic potential of the form ... 

Run a molecular dynamics simulation, then rotate the molecular system in the Molecular Coordinate System. This changes the coordinates of all atoms, but not the velocity vectors present at the end of the last molecular dynamics simulation. 

Molecular dynamics simulations have also been used to interpret phase behavior of DNA as a function of temperature. From a series of simulations on a fully solvated DNA hex-amer duplex at temperatures ranging from 20 to 340 K, a glass transition was observed at 220-230 K in the dynamics of the DNA, as reflected in the RMS positional fluctuations of all the DNA atoms [88]. The effect was correlated with the number of hydrogen bonds between DNA and solvent, which had its maximum at the glass transition. Similar transitions have also been found in proteins. 

Interatomic potentials. All molecular dynamics simulations and some MC simulations depend on the form of the interaction between pairs of particles (atoms... 

Because the cohesive energy of the fullerene Cyo is —7.29 eV/atom and that of the graphite sheet is —7.44 eV/atom, the toroidal forms (except torus C192) are energetically stable (see Fig. 5). Finite temperature molecular-dynamics simulations show that all tori (except torus Cm2) are thermodynamically stable. 

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