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Molecular dynamics simulation
Published in Zhigang Li, Nanofluidics, 2018
A notable feature of LAMMPS is the diverse force fields that can accommodate a great number of particles and models. The force fields integrated in LAMMPS range from simple pairwise potentials to complex molecular interactions for biological calculations. Almost all the potentials introduced in this Chapter can be found in LAMMPS. LAMMPS can model relatively simple, nanoscale water and other fluid flows. It can also study the dynamics of polymers and biomolecules (e.g., DNA and proteins) with the well-known CHARMM (chemistry at Harvard macromolecular mechanics), COMPASS (condensed-phase optimized molecular potentials for atomistic simulation studies), AMBER (assisted model building with energy refinement), and OPLS (optimized potential for liquid simulations) force fields. In addition to MD simulations, LAMMPS can also perform mesoscale simulations, such as DPD (dissipative particle dynamics) and DSMC (direct simulation Monte Carlo).
Classical Methods of Molecular Simulations of Disordered Materials
Published in Alexander Bagaturyants, Vener Mikhail, Multiscale Modeling in Nanophotonics, 2017
Alexander Bagaturyants, Vener Mikhail
Appendix: Software for MD Simulation Used in Calculations of Liquids and Disordered Condensed SystemsVASP (Viena Ab initio Simulation Package). Program package for calculations by DFT methods in the plane-wave basis set with periodic boundary conditions. Payware.CPMD (Car-Parrinello Molecular Dynamics). Program package for calculations by DFT methods (generalized gradient approximations) in the plane-wave basis set with periodic boundary conditions. CPMD is specially developed for parallelized MD calculations. As distinct from VASP. Freeware.AMBER (Assisted Model Building with Energy Refinement). This program is used for proteins, nucleic acids, and other classes of molecules. Payware.CHARMm (Chemistry at HARvard Macromolecular mechanics). The program is designed for calculations of various systems, from small molecules to solvated complexes of biological macromolecules. Payware.GROMACS (Groningen Simulation Package). Program package for calculations of biological macromolecules in aqueous solutions. This software in its characteristics is close to AMBER and CHARMm. Freeware.
Numerical Methods for Modeling of Nanosystems
Published in Alexander V. Vakhrushev, Computational Multiscale Modeling of Multiphase Nanosystems, 2017
The force field AMBER is used for proteins, nucleic acids, and a number of other classes of molecules. The filed CHARMM is intended for modeling different systems: from small molecules to solvated complexes of biological macromolecules.
Molecular packing analysis of the crystal smectic E phase of a benzothieno-benzothiophene derivative by a combined experimental / computational approach
Published in Liquid Crystals, 2021
Sebastian Hofer, Wolfgang Bodlos, Jiří Novák, Alessandro Sanzone, Luca Beverina, Roland Resel
Determination of the molecular packing within the SmE phase was performed by an experimental/computational approach. In the first step, the lattice constants were determined by indexing of the GIXD pattern. The crystallographic unit cell was used as an input for molecular dynamics (MD) simulation revealing the molecular packing. These simulations were carried out with the LAMMPS software package [25] using the CHARMM general force field version 3.0.1 [26]. Several thousand trial structures are generated by placing two randomly oriented molecules in an expanded (120%) unit cell. During the simulation run, the starting configuration was relaxed and reduced to the experimentally determined unit cell size. The resulting structures are then clustered based on similarities of the packing motifs. Each selected packing motif appeared multiple times at the respective total energy. The obtained packing motifs are judged by a comparison of observed (Fobs) and calculated structure factors (Fcalc) taken from the diffraction intensities on the basis of a reliability factor .
New development of atomic layer deposition: processes, methods and applications
Published in Science and Technology of Advanced Materials, 2019
Peter Ozaveshe Oviroh, Rokhsareh Akbarzadeh, Dongqing Pan, Rigardt Alfred Maarten Coetzee, Tien-Chien Jen
Other software, such as LAMMPS [38,106–109], NAMD [53], GROMACS, CHARMM [53] and AMBER [95,100] is also used for molecular dynamics simulation. For instance, by using LAMMPS for molecular dynamics simulation, Hieranian et al. [109] demonstrated that a single layer of molybdenum disulfide (MoS2) can effectively separate ions from water. They investigated the desalination of water through (MoS2) as a function of chemistry, pore size, hydrostatic pressure and geometry. To have efficient desalination, the sizes of pores should be such that both the water filtration and ion rejection are optimized. In one hand large pores do not effectively reject ions while very small pores permeation rate is low. Atomic layer deposition is effective in addressing such situations. Hu et al. [110] used MD to study and predict the influence of the initial surface composition and process temperature on the roughness of the surface, the growth rate and growth mode of the film deposition. Timo and Kari [111] in the study of the atomic layer deposition of alumina by TMA–H2O-process, they used MD simulation to study the water reaction mechanism with alumina to obtain more insight on the surface mechanisms and energetics which according to them is essential in the design and optimization of the ALD process.
Cytotoxicity activity, in silico molecular docking, protein- and DNA-binding study of a new Ni(II) Schiff base complex
Published in Journal of Coordination Chemistry, 2018
Niladri Biswas, Sumit Khanra, Arnab Sarkar, Shamee Bhattacharjee, Deba Prasad Mandal, Ankur Chaudhuri, Sibani Chakraborty, Chirantan Roy Choudhury
In silico binding mode analysis between synthesized nickel complex and duplex DNA was examined. The crystal structure of duplex DNA d(CGCGAATTCGCG)2 dodecamer (PDB ID: 1BNA) was retrieved from Protein Data Bank (PDB). All the water molecules were removed from the crystal structure. Hydrogen atoms and Momany-Rone partial charges were added to the duplex DNA. Duplex DNA and complex 1 were typed with CHARMM force-field [44, 45] before molecular docking study. Docking calculations were performed using CDOCKER program [46]. Molecular docking poses of complex 1 were ranked according to CDOCKER interaction energy. Finally energy minimization of the docked receptor-complex 1 was performed for further analysis. All procedures were carried out using Discovery Studio 3.5 software [47].