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VMD new file reader

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VMD new file reader

Molecular simulations of biological systems span a variety of programs, each with its own file format. To bring them all into a single viewer, VMD 2 has now a new molfile reader, which opens the HDF5-based H5MD trajectories written by GROMACS 2026, HOOMD-blue GSD soft-matter simulations, and OpenMiChroM / Nucleome Data Bank CNDB chromatin models, plus cheminformatics SDF chemical tables and a modernized trajectory reader. It also includes a rewritten GROMACS reader, that loads structures about three times faster. A companion helper loads only a specified subset of the structure, making cell-scale systems even easier to visualize and analyze.

Editorials

The Future of Biomolecular Modeling

A 2015 TCBG Symposium brought together scientists from across the Midwest to brainstorm about what's on the horizon for computational modeling. See a summary of what these experts foresee. Read more

Computer Modeling in Bionanotechnology-The History

Since 2001 Illinois scientists have innovatively used molecular dynamics to simulate biological molecules combined with nanodevices. It turns out that the computational microscope is the quintessential imaging tool for these bionano systems. By Lisa Pollack. Read more

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  • Workshop on Computational Biophysics 2026
  • Cade Duckworth awarded prestigious 2026-27 MCB/Biophysics Graduate Fellowship
  • Yupeng Li-Beckman Institute Graduate Fellow
  • Restricted Surface Diffusion of Cytochromes on Bioenergetic Membranes with Anionic Lipids


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    NAMD - A parallel, object-oriented molecular dynamics program. International Journal of Supercomputer Applications and High Performance Computing, 10:251-268, 1996.   
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