Omegagene is a molecular dynamics (MD) simulation engine tailored for enhanced conformational sampling methods with a non-Ewald electrostatic potential scheme. It employs the virtual-system-coupled multi-canonical MD (V-McMD) method to replace multi-process parallelized runs with multiple independent runs to avoid inter-node communication overhead. In addition, Omegagene adopts the non-Ewald-based zero-multipole summation method (ZMM) for treating electrostatic interactions, which makes it possible to eliminate Fourier space calculations altogether.
Back to Projects
Dec 2015
1 min read
Omegagene
Molecular dynamics simulation engine that uses enhanced conformational sampling methods with a non-Ewald electrostatic potential scheme