Selected article for: "force field and MD simulation"
Author: Yichun Wang; Usha Kadiyala; Zhibei Qu; Paolo Elvati; Christopher Altheim; Nicholas A. Kotov; Angela Violi; J. Scott VanEpps
Title: Anti-biofilm Activity of Graphene Quantum Dots via Self-Assembly with Bacterial Amyloid Proteins
  • Document date: 2019_2_19
    • ID: e0sxynb1_46
    Snippet: The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/550285 doi: bioRxiv preprint Molecular Dynamics (MD) Simulation. All the simulations were performed with the NAMD in explicit water using the classical all-atom force field CHARMM. A time step of 1 fs was employed to integrate the equations of motion. A cutoff of 1.2 nm was used in conjunction with the Particle Mesh Ewald method to.....
    Document: The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/550285 doi: bioRxiv preprint Molecular Dynamics (MD) Simulation. All the simulations were performed with the NAMD in explicit water using the classical all-atom force field CHARMM. A time step of 1 fs was employed to integrate the equations of motion. A cutoff of 1.2 nm was used in conjunction with the Particle Mesh Ewald method to evaluate long-range columbic forces. The systems were minimized for 1000 steps before the production runs. Single peptide simulations for a total or more than 650 ns, were performed in a canonical ensemble (300 K, with a time constant of 1 ps) in a cubic simulation box with side 7.5 nm. Production runs of the PSMα1 dimers were performed in a canonical ensemble in a cubic simulation box with a side of 10 nm.

    Search related documents:
    Co phrase search for related documents
    • atom force and long range: 1
    • atom force and nm cutoff: 1
    • atom force and Particle Mesh Ewald method: 1, 2
    • atom force and production run: 1
    • atom force field and canonical ensemble: 1
    • atom force field and long range: 1
    • atom force field and nm cutoff: 1
    • atom force field and Particle Mesh Ewald method: 1, 2
    • atom force field and production run: 1
    • canonical ensemble and production run: 1
    • long range and motion equation: 1
    • long range and Particle Mesh Ewald method: 1, 2, 3, 4
    • motion equation and Particle Mesh Ewald method: 1
    • nm cutoff and Particle Mesh Ewald method: 1, 2