bondrewd / cgdyntest

GENESIS cgdyn MD files and analysis scripts

This repository is used to share simulation data for the publication of:

• Jung J, Tan C, and Sugita Y (2023) GENESIS CGDYN: large-scale coarse-grained molecular dynamics simulation with dynamic load balancing for heterogeneous biomolecule systems

Software

In this work we report the development of GENESIS CGDYN, which can be accessed from:

• GENESIS CGDYN: https://github.com/genesis-release-r-ccs/genesis-2.1.0beta_cgdyn

For MD system preparation and analysis, use the following program:

• GENESIS-cg-tool: https://github.com/genesis-release-r-ccs/genesis_cg_tool

Directory structure

Benchmark systems

• dna_benchmark_hokusai: benchmark of duplicated DNA system on supercomputer server Hokusai (RIKEN-RCCS) (Supporting Table 1)
• dna_benchmark: benchmark of duplicated DNA system on local PC clusters (Supporting Figure 3)
• dry_martini_benchmark: benchmark of Martini lipid system on supercoputer Fugaku (Supporting Figure 8a)
• fugaku_droplet_benchmark/: benchmark of large-scale protein droplet simulations on supercomputer Fugaku (Supporting Figure 8b)
• others: benchmark of previously-reported systems (Tan C et al. PLoS Comput Biol, 2022) (Supporting Figure 4)

Application systems

• application01_two_droplet_fusion/: MD simulations of two-droplet fusion system (Figure 3)
• application02_multiple_droplet_fusion/: MD simulations of near-realistic-scale multiple-droplet systems (Figure 4)

Analysis scripts are included in each directory.

Structures:

Application 1: Two droplet system:

• Initial structure: application01_two_droplet_fusion/00_MD/rst/tdp43_1000_minimized.rst (MD restart file)
• Final structure: application01_two_droplet_fusion/00_MD/output/tdp43_test1_frame10000_with_clustering_labels.cif
• Intermediate structures: application01_two_droplet_fusion/00_MD/output/tdp43_test1_frame*_with_clustering_labels.cif

Application 2: Multiple droplet system:

High density system

• Initial structure: application02_multiple_droplet_fusion/00_MD/output_high_density/rCG_Droplets_50_50_50_100_b100_f85_g20_d0_rho0.56_s_5_d_5_md_00_frame_00000.gro
• Final structure: application02_multiple_droplet_fusion/00_MD/output_high_density/rCG_Droplets_50_50_50_100_b100_f85_g20_d0_rho0.56_s_5_d_5_md_60_frame_02000.gro
• Ohter intermediate structure: application02_multiple_droplet_fusion/00_MD/output_high_density/rCG_Droplets_50_50_50_100_b100_f85_g20_d0_rho0.56_s_5_d_5_md_*_frame_*.gro

Low density system

• Initial structure: application02_multiple_droplet_fusion/00_MD/output_low_density/rCG_Droplets_50_50_50_100_b100_f85_g20_d0_rho0.56_s_5_d_2_md_00_frame_00000.gro
• Final structure: application02_multiple_droplet_fusion/00_MD/output_low_density/rCG_Droplets_50_50_50_100_b100_f85_g20_d0_rho0.56_s_5_d_2_md_60_frame_02000.gro
• Ohter intermediate structure: application02_multiple_droplet_fusion/00_MD/output_low_density/rCG_Droplets_50_50_50_100_b100_f85_g20_d0_rho0.56_s_5_d_2_md_*_frame_*.gro