[124]. They are widely used in molecular dynamics software packages and allow for efficient and reliable simulations of molecular systems over time. The algorithms used in molecular dynamics need the initial position of atoms and the forces that act on them to solve Newton's equations of motion...
Comparison of the Performance of a Program for Molecular Dynamics Simulations of Liquids on Different Computersdoi:10.1021/cm00021a044ENANTIOMERIZATIONDYNAMIC COMPLEXATION GAS CHROMATOGRAPHYHOMOFURANThe absorbance of a solvent polymeric bulk optode membrane in contact with sapphire as a wave-guide is ...
In this study, molecular dynamics simulations were performed to investigate the effects on single-stranded polynucleotide encapsulation by chitosan and the underlying interaction mechanism between polynucleotide and different types of chitosan with atomic details. It was found that the functional groups of c...
A Molecular Dynamics Computer Simulation Performance Comparison of Java Versus CJavaMolecular dynamicsComputer simulationThe relative performance of molecular dynamics (MD) computer simulations of fluids written in ANSI C is compared to that achieved by a comparable program written in Java. The performance...
Beside the experimental works on development of MPSs, computational studies can be useful to understand the interaction at molecular level, and manipulate the functional groups for preparation of advanced porous materials for environmental applications. Molecular dynamics simulation is a great modelling tool...
NMR data are particularly useful, as the many receptor and ligand conformations sampled by molecular dynamics simulations can be used to predict NMR measurements like spin relaxation, permitting direct comparison between experimental and theoretical techniques. Indeed, a number of studies have shown good...
Domain-localized linear interpolation of the atoms from a molecular dynamics simulation performed with MODELLER in ePMV and a hinged bone skeleton (host) for large domain motion was used to morph between the two experimental conformations, host-based vibration was applied to the ligand to imply ...
Figure 7. Comparison of GROMACS 2019 to GROMACS 2020 using three multi-GPU simulation examples. The graph in Figure 7 compares the performance of the new GROMACS 2020 version (with the earlier optimizations enabled) with the previous 2019.5 version, for each of the test cases. The graph...
Our complex example material is semicrystalline P3HT, and we were able to use our method, along with experimental INS data, to make a valuable, direct comparison between experimental and simulated low energy dynamics. Such a direct comparison with molecular dynamics simulations is not possible with ...
(MD) simulations. Integrating two widely used modeling programs, namely NAMD and VMD, we have created a robust, user-friendly software, QwikMD, which enables novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers. ...