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Samples
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:Author: Kota Kasahara

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Sample files
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Some sample simulation data are attached.

In following instruction, it is assumed that the variable $OMEGATK indicates the path to the *omega_toolkit*.
And the binary *omegagene* is placed in a directory in ${PATH}, and the library files *libCelesteCUDA.so* and *libCelesteCore.a* are placed in ${LD_LIBRARY_PATH} directories.

NVE calculation (Trp-cage)
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Move to the directory *cal01_nve/run00001*.

And execute the bash file::

  bash 1_generate_velocities.bash

In this shell, the initial velocities are generated. See the output::

  number of atoms: 13277
  Number of rigid units: 4495
  TEMPERATURE:300.0
  [ 2.05517825e-11 4.44033144e-11 -9.32866839e-11]`

The last line indicates the momentum of COM in each axis.

Next, check the simulation setting in *system.cfg* and *atom_groups.inp*::

  vi system.cfg
  vi ../atom_groups.inp

Generate the input binary file::

  bash 2_mdinput_gen.bash

The log is output in *mdinpgen.out*::

  size: buf_pos_rest: 4
  size: buf_group_coord: 0
  End

Then, execute omegagene. Before that, check the setting file *md.cfg*::

  vi md.cfg

Execute it::

  bash 3_submit.bash

The directory *run00002* is for test of restarting the calculation in *run00001*::

  cd ../run00002
  diff system.cfg ../run00001/
  diff md.cfg ../run00001/
  bash 4_mdinput_gen_2.bash
  bash 5_submit_2.bash

Check the accordance of the energy values at the last of *run00001* and the first of *run00002*.


Other ensembles
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Some other samples can be performed in a similar way.

* *cal02_nvt* for NVT calculation (Trp-cage)
* *cal03_vmcmd* for V-McMD calculation (Trp-cage)
* *cal04_aus* for V-AUS calculation (2 Alanine-pentapeptides)

