High-performance molecular dynamics simulation on GPUs for advanced simulation methods
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Oct 2, 2026 - Rich Text Format
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charmm36
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A collection of GROMACS molecular dynamics simulation projects featuring protein-only and protein–ligand systems using CHARMM36, AMBER99SB, and physiological ionic conditions.
linux bioinformatics molecular-dynamics computational-biology molecular-simulation drug-discovery gromacs protein-ligand-interactions protein-ligand charmm36 amber99sb
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Jul 31, 2026 - Rich Text Format
Three Nigella sativa alkaloids (indazoles nigellidine, nigellicine; isoquinoline nigellimine) vs S. aureus FtsZ (PDB 3VOA): ADMET screening; docking with Vina, AutoDock4, GNINA, DiffDock-L (redock RMSD 0.307 Å); 4I55 tubulin counter-screen; 100 ns MD; MM-GBSA −13.28 ± 0.97 kcal/mol (SD). Computational predictions only.
cheminformatics molecular-dynamics vmd drug-discovery openbabel gromacs molecular-docking autodock4 autodock-vina gmx-mmpbsa protox staphylococcus-aureus chimerax gnina diffdock mm-gbsa cgenff swissadme charmm36 ftsz
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Sep 26, 2026
GROMACS MD for Zn2+ metalloproteins with CHARMM36: auto-detects zinc and ligand, runs on laptop or SLURM GPU, with a metal-coordination analysis tutorial.
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Oct 2, 2026 - Shell
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