11 research outputs found
Elastic Property of Dynein Motor Domain Obtained from All-Atom Molecular Dynamics Simulations in Explicit Water
Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions
Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling
Shinji Iida, Tadaaki Mashimo, Takashi Kurosawa, Hironobu Hojo, Hiroya Muta, Yuji Goto, Yoshifumi Fukunishi, Haruki Nakamura, and Junichi Higo, "Variation of free‐energy landscape of the p53 C‐terminal domain induced by acetylation: Enhanced conformational sampling", Journal of Computational Chemistry, 37, 2687-2700, Wiley, 201
Elastic Property of Dynein Motor Domain Obtained from All-Atom Molecular Dynamics Simulations in Explicit Water
Miscellaneous Topics in Computer-Aided Drug Design: Synthetic Accessibility and GPU Computing, and Other Topics
Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions
A molecular dynamics (MD) simulation
program for biological macromolecules
was implemented with a non-Ewald scheme for long-ranged electrostatic
interactions and run on a general purpose graphics processing unit
(GPU). We recently developed several non-Ewald methods to compute
the electrostatic energies with high precision. In particular, the
zero-dipole summation (ZD) method, which takes into account the neutralities
of charges and dipoles in a truncated subset, enables the calculation
of electrostatic interactions with high accuracy and low computational
cost, and its algorithm is simple enough to be implemented in a GPU.
We developed an MD program with the space decomposition algorithm,
myPresto/psygene, and applied it to several biological macromolecular
systems with GPUs implementing the ZD method. Rapid computing performance
with high accuracy was obtained