Fig. 1: Shape-based coarse-grained 2 (SBCG2) HIV-1 capsid.

a View of the HIV-1 CA monomer, left, colored by domain. On the right, three corresponding SBCG2 models of HIV-1 CA with increasing granularity. Granularity, in this case, refers to the number of beads employed to model the structure. b Full view of the SBCG2 HIV-1 conical capsid, shown from two perspectives. c Clipped view of the SBCG2 HIV-1 conical capsid, shown from two perspectives. For panels b and c, protein is shown as vdW beads, with the CA amino-terminal domains colored tan and the CA carboxy-terminal domains colored blue. IP6 beads are shown as orange vdW spheres^46,47. d, e Performance benchmarks with NAMD3⁴⁵, simulating the HIV-1 conical capsid shown in panels c and d. Benchmarks were performed with one CPU per GPU employed. For both benchmarks, an identical configuration was employed, and only the usage of PME for long-range electrostatics varied. The time step employed was 48 fs per step; Langevin γ was set to 2.0 ps⁻¹; bonded interactions were evaluated every time step and nonbonded interactions were evaluated every other time step. d NAMD3 GPU benchmarks, utilizing NVIDIA V100s, with PME on. Peak performance of nearly 300 ns per day represents a threefold speedup over peak CPU-only simulation performance, which employed as many as ten compute nodes (Supplementary Fig. 2). e NAMD3 GPU benchmarks, utilizing NVIDIA V100s, with PME off. Remarkably, for three and four GPUs per simulation, we exceed one microsecond per day simulation performance (dashed line). Benchmarks reported are the mean value of the six benchmark metrics reported by NAMD3⁴⁵ for each simulation.