![]() Last update on Novemomegagene: a GPU-accelerated molecular dynamics simulator with enhanced conformational samplingĪ new engine, “omegagene”, has joined in myPresto program suits for more effective conformational sampling with GPU-accelerated molecular dynamics simulation. ![]() Mashimo, T., Fukunishi, Y., Kamiya, N., Takano, Y., Fukuda, I., Nakamura, H. Last update on Februpsygene-G: Protein dYnamics SimulatinG ENginE for GPUĪ rapid molecular dynamics simulation program, which uses our original non-Ewald algorithm (Zero-Dipole summation method ) for electrostatic interactions, has been developed for a single and multiple GPUs (Graphics Processing Units) with the space decomposition algorithm. ![]() The generalized ensemble method is useful to calculate the free energy surface.įukunishi, Y., Mikami, Y., Nakamura, H. Cosgene can calculate the protein-compound binding free energy by the filling potential method. In addition, cosgene can calculate the generalized ensemble like multicanonical ensemble. Cosgene can calculate NVE, NVT and NPT ensemble with various boundary conditions. AMBER and CHARMM force fields are available. Molecular dynamics simulation cosgene: COnformation SamplinG ENginEĪ molecular dynamics simulation program for protein, DNA, chemical compound, protein-ligand complex. MyPresto Protal is a graphic user interface (GUI) program for myPresto and GROMACS, available for Windows, MAC and Linux (all 64bit).Įasy myPresto is a graphic user interface (GUI) program for myPresto, available for Windows, MAC and Linux (all 64bit). ![]() Simple software package with graphic interface myPresto Portal Synthetic accessibility estimation and Drug design.Structure preparation and file format conversion for small molecules, etc.Simple software package with graphic interface. ![]()
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