              sarscov2-10880334-no-water-no-ion-glueCA Trajectory
                              D. E. Shaw Research
                                 March 27, 2020

100-microsecond simulation of the apo enzyme started from the apo enzyme
structure determined by X-ray crystallography (PDB entry 6Y84) with frames
saved every 1-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
sub-directory containing DCD files, a structure file in Maestro
format, and a copy of the license file.  The DCD directory
sarscov2-10880334-no-water-no-ion-glueCA contains segments of
the trajectory sarscov2-10880334-no-water-no-ion-glueCA-nnn.dcd
in DCD form.  The start time for each DCD segment is given in the
sarscov2-10880334-no-water-no-ion-glueCA/sarscov2-10880334-no-water-no-ion-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.

License
=======

The sarscov2-10880334-no-water-no-ion-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 sarscov2-10880334-no-water-no-ion-glueCA/*.mae
  sarscov2-10880334-no-water-no-ion-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.
