<jupyter_start><jupyter_text>VMD[VMD](http://www.ks.uiuc.edu/Research/vmd/) is a widely used MD visualization tool. <NAME> developed a [GSD file reader plugin for VMD](https://github.com/mphoward/gsd-vmd). See the plugin's README for installation instructions.Set up a simple Lennard-Jones particle simulation:<jupyter_code>hoomd.context.initialize('--mode=cpu --notice-level=1');
system = hoomd.init.create_lattice(unitcell=hoomd.lattice.sq(a=2.0), n=5);
nl = hoomd.md.nlist.cell();
lj = hoomd.md.pair.lj(r_cut=3.0, nlist=nl);
lj.pair_coeff.set('A', 'A', epsilon=1.0, sigma=1.0);
all = hoomd.group.all();
hoomd.md.integrate.mode_standard(dt=0.001);
hoomd.md.integrate.langevin(group=all, kT=1.0, seed=987);<jupyter_output>HOOMD-blue v2.1.4 CUDA (8.0) DOUBLE HPMC_MIXED MPI SSE SSE2 SSE3 SSE4_1 SSE4_2 AVX 
Compiled: 03/09/2017
Copyright 2009-2016 The Regents of the University of Michigan.
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You are using HOOMD-blue. Please cite the following:
* <NAME>, <NAME>, and <NAME>. "General purpose molecular dynamics
  simulations fully implemented on graphics processing units", Journal of
  Computational Physics 227 (2008) 5342--5359
* <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, <NAME>, and
  <NAME>. "Strong scaling of general-purpose molecular dynamics simulations
  on GPUs", Computer Physics Communications 192 (2015) 97--107
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HOOMD-blue is running on the CPU<jupyter_text>Write out the trajectory to GSD. GSD files contain all particle properties in the first frame. By default, they store position and orientation data (only if it changes) in subsequent frames.<jupyter_code>d = hoomd.dump.gsd("dump.gsd", period=100, group=all, overwrite=True);
hoomd.run(1000, quiet=True);<jupyter_output><empty_output>
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{'chain_length': '2', 'dir': 'jupyter-structured-clean-dedup', 'id': '74668', 'license': 'BSD-3-Clause', 'n_tokens_mistral': 662, 'n_tokens_neox': 602, 'n_words': 168, 'path': 'Analysis - Visualization - VMD.ipynb', 'repo_name': 'jennyfothergill/hoomd-examples', 'size': '1769'}