               sarscov2-11021571-no-water-zinc-glueCA Trajectory
                              D. E. Shaw Research
                                 April 29, 2020

10-microsecond simulation of the trimeric SARS-CoV-2 spike glycoprotein with
additional loop structures and glycan chains initiated in a partially opened
state (PDB entry 6VYB) with frames saved every 1.2-nanosecond.

The suffix of the distribution directory's name encodes the selection of
frames from the full trajectory dataset:

  -all               : all frames, all atoms
  -10                : every 10th frame, all atoms
  -100               : every 100th frame, all atoms
  -protein           : all frames, protein atoms only
  -protein-zma-noh   : all frames, (protein or resname ZMA) and noh atoms
  -c-alpha           : all frames, alpha carbon atoms only
  -first             : all atoms, initial segment of frames
  -short             : all atoms, representative segment of frames
  -no-water-no-ion   : all frames, excluding water and ions

Suffix modifiers, such as 'first' or 'short', can be combined with the above
forms to indicate that a representative time segment of the full dataset is
being provided.

Each distribution directory contains a README.txt file, a structure
file in Maestro format, a structure file in PDB format, a structure
file in PSF format, and a copy of the license file.  The DCD
directory sarscov2-11021571-no-water-zinc-glueCA contains segments
of the trajectory sarscov2-11021571-no-water-zinc-glueCA-nnn.dcd
in DCD form.  The start time for each DCD segment is given in the
sarscov2-11021571-no-water-zinc-glueCA/sarscov2-11021571-no-water-zinc-glueCA_times.csv
file, comma separated value file that is both human readable and
spreadsheet compatible. The system.mae file contains the structure
information used in the simulation.  There is also a reduced structure
file in the DCD directory that can be different from the simulation
structure file; for example, the reduced structure file for trajectories
consisting of only protein atoms, contains only the appropriate atoms. The
sarscov2-11021571-no-water-zinc-glueCA/sarscov2-11021571-no-water-zinc-glueCA_energies.csv
file contains energy information for each frame.

License
=======

The sarscov2-11021571-no-water-zinc-glueCA trajectory dataset is released
under a Creative Commons Attribution 4.0 International Public License a copy of
which is contained in the file CC4_License.txt provided in this distribution.

Citation
========

The use of any trajectory data in any reports or publications of results
obtained with the trajectory data should be acknowledged by including a
citation to:

  D. E. Shaw Research, "Molecular Dynamics Simulations Related to
  SARS-CoV-2," D. E. Shaw Research Technical Data, 2020.
  http://www.deshawresearch.com/resources_sarscov2.html/

Viewing in VMD
==============

This trajectory may be viewed using the VMD version 1.8.7 or later (or
any other tool capable of reading files in DCD and Maestro format).
The VMD software is available from the Theoretical and Computational
Biophysics Group at the University of Illinois at Urbana-Champaign,
http://www.ks.uiuc.edu/Research/vmd

  Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular
  Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.

To view the full trajectory, change to the unpacked trajectory directory
and use the command:

  $ vmd sarscov2-11021571-no-water-zinc-glueCA/*.mae
  sarscov2-11021571-no-water-zinc-glueCA/*.dcd

Depending on the number of frames in the dataset, and the amount of memory
on your system, you might need to pass only a subset of the DCD files on
the command line.
