Putting it all together: Running a GOMC Simulation
==================================================

It is strongly recommended that you download the test system provided at `GOMC Website`_ or `Our Github Page`_

.. _GOMC Website: http://gomc.eng.wayne.edu/downloads.html

.. _Our Github Page: https://github.com/GOMC-WSU/GOMC_Examples/tree/master

Run different simulation types in order to become more familiar with different parameter and configuration files (\*.conf).

To recap the previous examples, a simulation of isobutane will be completed for a single temperature point on the saturated vapor-liquid coexistence curve.

The general plan for running the simulation is:

1. Build GOMC (if not done already)
2. Copy GOMC executable to build directory
3. Create scripts, PDB, and topology file to build the system, plus in.dat file and parameter files to prepare for runtime
4. Build finished PDBs and PSFs using the simulation.
5. Run the simulation in the terminal.
6. Analyze the output.

Please, complete steps 1 and 2; then, traverse to the directory, which should now contain a single file "GOMC_CPU_GEMC". Next, six files need to be made:

- PDB file for isobutane
- Topology file describing isobutane residue
- Two ``*.inp`` packmol scripts to pack two system boxes
- Two *TCL* scripts to input into ``PSFGen`` to generate the final configuration

``isobutane.pdb``

.. code-block:: text

  REMARK   1 File  created   by  GaussView   5.0.8
  ATOM          1       C1  ISB          1   0.911   -0.313    0.000  C
  ATOM          2       C2  ISB          1   1.424   -1.765    0.000  C
  ATOM          3       C3  ISB          1  -0.629   -0.313    0.000  C
  ATOM          4       C4  ISB          1   1.424    0.413   -1.257  C
  END

``Top_Branched_Alkane.inp``

.. code-block:: text

  * Custom top file -- branched alkanes
  *
  MASS     1    CH3      15.035 C !
  MASS     2    CH1      13.019 C !

  AUTOGENERATE ANGLES DIHEDRALS

  RESI   ISB   0.00               !  isobutane { TraPPE }
  GROUP
  ATOM    C1    CH1       0.00    !  C3\
  ATOM    C2    CH3       0.00    !     C2-C1
  ATOM    C3    CH3       0.00    !  C4/
  ATOM    C4    CH3       0.00    !
  BOND    C1  C2   C1  C3   C1  C4
  PATCHING FIRS NONE LAST NONE
  END


``pack_box_0.inp``

.. code-block:: text

  tolerance   3.0
  filetype    pdb
  output      STEP2_ISB_packed_BOX_0.pdb

  structure     isobutane.pdb
  number        1000
  inside cube   0.  0.  0.  68.00
  end structure

``pack_box_1.inp``

.. code-block:: text

  tolerance   3.0
  filetype    pdb
  output      STEP2_ISB_packed_BOX_1.pdb

  structure     isobutane.pdb
  number        1000
  inside cube   0.  0.  0.  68.00
  end structure

``build_box_0.inp``

.. code-block:: text

  package require psfgen

  topology  ./Top Branched Alkane.inp segment ISB {
    pdb     ./STEP2_ISB_packed_BOX_0.pdb
    first   none
    last    none
  }
  coordpdb  ./STEP2 ISB_packed_BOX_0.pdb ISB

  writepsf  ./STEP3_START_ISB_sys_BOX_0.psf
  writepdb  ./STEP3_START_ISB_sys_BOX_0.pdb

``build_box_1.inp``

.. code-block:: text

  package require psfgen

  topology  ./Top Branched Alkane.inp segment ISB {
    pdb     ./STEP2_ISB_packed_BOX_1.pdb
    first   none
    last    none
  }
  coordpdb  ./STEP2 ISB_packed_BOX_1.pdb ISB

  writepsf  ./STEP3_START_ISB_sys_BOX_1.psf
  writepdb  ./STEP3_START_ISB_sys_BOX_1.pdb


These files can be created with a standard Linux or Windows text editor. Please, also copy a Packmol executable into the working directory.

Once those files are created, run in the terminal:

.. code-block:: bash

  $ ./packmol   <   pack_box_0.inp
  $ ./packmol   <   pack_box_1.inp

This will create the intermediate PDBs.

Then, run the PSFGen scripts to finish the system using the following commands:

.. code-block:: bash

  $ vmd -dispdev text < ./build_box_0.inp
  $ vmd -dispdev text < ./build_box_1.inp

This will create the intermediate PDBs.

To run the code a few additional things will be needed:

- A GOMC Gibbs ensemble executable 
- A control file
- Parameter files

Enter the control file (in.conf) in the text editor in order to modify it. Example files for different simulation types can be found in previous section.

Once these four files have been added to the output directory, the simulation is ready.

Assuming the code is named GOMC_CPU_GEMC, run in the terminal using:

.. code-block:: bash

  $ ./GOMC CPU GEMC in.conf > out_ISB_T_330.00_K_RUN_0.log &

For running GOMC in parallel, using openmp, run in the terminal using:

.. code-block:: bash

  $ ./GOMC CPU GEMC +p4 in.conf > out_ISB_T_330.00_K_RUN_0.log&

Here, 4 defines the number of processors that will be used to run the simulation in parallel. 

Progress can be monitored in the terminal with the tail command:

.. code-block:: bash

  $ tail -f out_ISB.log

.. attention:: Congratulations! You have examined a single-phase coexistence point on the saturated vapor-liquid curve using GOMC operating in the Gibbs ensemble.

.. figure:: static/isobutane_result.png
  :figwidth: 100%
  :width: 100%
  :align: center

  Repeating this process for multiple temperatures will allow you to obtain the following results.