The overall aim of this study is to calculate some water properties in the single wall carbon naotubes (SWCNT) and compare them to the bulk water properties to investigate the deviation of water properties inside the SWCNT from those in the bulk. Here some physical and transport properties of water molecules in the single wall carbon nanotube were reported by performing molecular dynamics (MD) ...

Here we report on the performance of GROMACS 4.6 on the SuperMUC cluster at the Leibniz Rechenzentrum in Garching. We carried out benchmarks with three biomolecular systems consisting of eighty thousand to twelve million atoms in a strong scaling test each. The twelve million atom simulation system reached a performance of 49 nanoseconds per day on 32,768 cores.

Using GROMACS (a molecular dynamics package) we simulate ionic copolymers and compare the numerical results with those obtained by the lattice Monte Carlo simulations. While the results are qualitatively similar for both methods, the simulation times are significantly longer for the molecular dynamics simulations than those for the corresponding Monte Carlo runs.

The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well-exploited with a combination of single instruction multiple data, multithreading, and message passing interface (MPI)-based single program multiple data/multiple program multiple data parallelism while gra...

To reduce the number of replicas required in the conventional replica exchange method for huge systems, recently the replica exchange with solute tempering (REST) method was proposed. Here we showed that a variant of REST realized by rescaling the force-field parameters can be performed with GROMACS 4 without changing the code. We tested the variant REST for alanine dipeptide and an N-terminal ...

Определено оптимальное соотношение винпоцетина и b-циклодекстрина в лекарственной форме (1:2 или 1:5) по результатам моделирования молекулярной динамики высвобождения действующего вещества водную среду. Молекулярную динамику из поливинилпирролидона моделировали течение 100 нс с использованием программы Gromacs 2019 силовом поле Gromos 54a7. Равновесие при высвобождении исследуемого носителя нас...

Background: The outbreak of the COVID-19 pandemic caused by SARS-CoV-2 has triggered intense scientific research into possible therapeutic strategies that can combat ravaging disease. One such is inhibition an important enzyme affects physiological process virus. enzyme, Guanine-N7 Methyltransferase responsible for capping mRNA to conceal it from host’s cellular defense. aim study: This study a...

The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on underexplored regions of configuration space while maintai...