Merge pull request #288 from akohlmey/moltemplate-1.40

This is an example of how to use the OPLSAA force-field in LAMMPS

(using moltemplate.sh and Jason Lambert's oplsaa_moltemplate.py conversion tool)

This example also shows how to use moltemplate in combination with PACKMOL.

(PACKMOL is a useful program for generating atomic coordinates. In this example,

 moltemplate.sh is only used to create the topology, force-field and charges,

 and PACKMOL generates the coordinates, which moltemplate reads (in "step 1").

 Moltemplate can also be used for generating atomic coordinates, especially

 for mixing many small molecules together, as we do in this example.  However 

 I wanted to demonstrate how to combine PACKMOL with moltemplate.sh.

 In some other scenarios, such as protein solvation, PACKMOL does a much

 better job than moltemplate.)

As of 2014-4-06, this code has not been tested for accuracy.

(See the WARNING.TXT file.)

step 1)

To build the files which LAMMPS needs, follow the instructions in:

README_setup.sh

step 2)

To run LAMMPS with these files, follow these instructions:

README_run.sh

# -------- REQUIREMENTS: ---------

#  You must define your MOLTEMPLATE_PATH environment variable

#  and set it to the "common" subdirectory of your moltemplate distribution.

#  (See the "Installation" section in the moltemplate manual.)

# Create LAMMPS input files this way:

cd moltemplate_files

  # Create the "oplsaa.lt" file which moltemplate will need

  cd oplsaa_lt_generator/

  oplsaa_moltemplate.py  oplsaa_subset.prm

  mv -f oplsaa.lt ..

  cd ..

  # run moltemplate

  moltemplate.sh system.lt

  # This will generate various files with names ending in *.in* and *.data. 

  # Move them to the directory where you plan to run LAMMPS (in this case "../")

  mv -f system.data system.in* ../

  # Optional:

  # The "./output_ttree/" directory is full of temporary files generated by 

  # moltemplate.  They can be useful for debugging, but are usually thrown away.

  rm -rf output_ttree/

  # Optional:

  # Delete the "oplsaa.lt" file:

  rm -f oplsaa.lt

cd ../

This is an example of how to use the OPLSAA force-field in LAMMPS

(using moltemplate.sh and Jason Lambert's oplsaa_moltemplate.py conversion tool)

This example also shows how to use moltemplate in combination with PACKMOL.

(PACKMOL is a useful program for generating atomic coordinates. In this example,

 moltemplate.sh is only used to create the topology, force-field and charges,

 and PACKMOL generates the coordinates, which moltemplate reads (in "step 1").

 Moltemplate can also be used for generating atomic coordinates, especially

 for mixing many small molecules together, as we do in this example.  However 

 I wanted to demonstrate how to combine PACKMOL with moltemplate.sh.

 In some other scenarios, such as protein solvation, PACKMOL does a much

 better job than moltemplate.)

As of 2014-12-19, this code has not been tested for accuracy.

(See the WARNING.TXT file.)

step 1)

To build the files which LAMMPS needs, follow the instructions in:

README_setup.sh

step 2)

To run LAMMPS with these files, follow these instructions:

README_run.sh

# -------- REQUIREMENTS: ---------

#  You must define your MOLTEMPLATE_PATH environment variable

#  and set it to the "common" subdirectory of your moltemplate distribution.

#  (See the "Installation" section in the moltemplate manual.)

# Create the coordinates of the atoms using PACKMOL

cd packmol_files

  packmol < mix_ethylene+benzene.inp

  mv -f system.xyz ../moltemplate_files/

cd ..

# Create LAMMPS input files this way:

cd moltemplate_files

  # Create the "oplsaa.lt" file which moltemplate will need

  cd oplsaa_lt_generator/

  oplsaa_moltemplate.py  oplsaa_subset.prm

  mv -f oplsaa.lt ..

  cd ..

  # run moltemplate

  moltemplate.sh -xyz system.xyz system.lt

  # This will generate various files with names ending in *.in* and *.data. 

  # Move them to the directory where you plan to run LAMMPS (in this case "../")

  mv -f system.data system.in* ../

  # Optional:

  # The "./output_ttree/" directory is full of temporary files generated by 

  # moltemplate.  They can be useful for debugging, but are usually thrown away.

  rm -rf output_ttree/

  # Optional:

  # Delete the "oplsaa.lt" file:

  rm -f oplsaa.lt

cd ../

# -------- REQUIREMENTS: ---------

#  You must define your MOLTEMPLATE_PATH environment variable

#  and set it to the "common" subdirectory of your moltemplate distribution.

#  (See the "Installation" section in the moltemplate manual.)

# Create LAMMPS input files this way:

cd moltemplate_files

  # Create the "oplsaa.lt" file which moltemplate will need

  cd oplsaa_lt_generator/

  oplsaa_moltemplate.py  oplsaa_subset.prm

  mv -f oplsaa.lt ..

  cd ..

  # run moltemplate

  moltemplate.sh system.lt

  # This will generate various files with names ending in *.in* and *.data. 

  # Move them to the directory where you plan to run LAMMPS (in this case "../")

  mv -f system.data system.in* ../

  # Optional:

  # The "./output_ttree/" directory is full of temporary files generated by 

  # moltemplate.  They can be useful for debugging, but are usually thrown away.

  rm -rf output_ttree/

  # Optional:

  # Delete the "oplsaa.lt" file:

  rm -f oplsaa.lt

cd ../