If the total energy drifts more than some predetermined amount during the course of the simulation, then all the velocities can be rescaled to shift the total energy back to its initial value. Alternatively, one can use a thermostat to maintain the temperature at a desired value; see Frenkel ...
The simulation trajectory demonstrates that the oligosaccharide diffuses around the protein and eventually identifies and binds to the biologically designated binding site of galectin-3 in real time. The simulated bound pose correlates with the crystallographic pose with atomic-level accuracy and ...
In the MD simulation performed, we have added an EF as an external Coulomb force acting on every atom in the system. We analyzed the effect of the EF strength starting from 20 MV/m up to 300 MV/m. The rationale for the selection of this range of field strength is both theoretical and...
The effect of the tacticity of poly methyl methacrylate (PMMA) on the morphology of free volume in PMMA membranes was studied by using a molecular dynamics simulation technique. The chain flexibility, chain interaction, end-to-end distance of a chain and the time course of the free volume ...
Molecular-dynamic simulation of low-temperature plastic deformation ( T def = 50 K, T def / T g ≤ 0.3) is studied for glassy polymethylene under the regime of active uniaxial compression and tension for a cell composed of 64 chains containing 100 -CH 2 groups in each (as united atoms)...
During the course of a molecular dynamics simulation, the electrostatic and van der Waals forces produced by ligand atoms are turned down gradually enough to avoid undesirable artifacts. Eventually, the ligand is no longer able to interact with the protein or solvent. For all practical purposes, ...
parameters chosen for the MD simulations reproduces the membrane geometry at a good level. On the contrary, the electron density profile of Wi-A and Wi-N clearly showed that the preferable locations for withanolides (in due course of MD simulation) was close to lipid head group region (Fig....
For full dynamic load balancing the boundaries be- tween the cells need to move during the simulation. For 1D domain decomposition this is trivial, but for a 3D decomposition the cell boundaries in the last two dimen- sions need to be staggered along the first dimensions to ...
transition path sampling and diffusive barrier crossing to simulaterare events dissipative particle dynamic as a course-grained simulation technique novel schemes to compute the long-ranged forces hamiltonian and non-hamiltonian dynamics in the context constant-temperature and constant-pressure molecular ...
Of course, in materials with low polarity the dielectric relaxations are very weak and not easily detected. The main relaxation processes observed in polymeric systems will be analysed in the next sections. It must be pointed that, besides the example given here for the mechanical and elec-tri...