lammps/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane16eed7a05366master
lammps/tools/moltemplate/examples/all_atom_examples/force_field_OPLSAA/hexadecane
16eed7a05366master
hexadecane
hexadecane
README.TXT
README.TXT
This example is a simple simulation of many long alkane chains (hexadecane) in a
box at room temperature and atmospheric pressure. Please read "WARNING.TXT".
NOTE: This particular file contains instructions for how to build molecules
using the OPLSAA force-field. However, moltemplate is not limited to
OPLSAA. You can use other force-fields, or define your own force-fields
(or provide a list of bonded interactions explicitly).
-------- INSTRUCTIONS: ---------
1) Download the "oplsaa.prm" file containing the OPLS force field
parameters. I do not have permission to distribute those parameters,
but you can download them from one of these URLS:
http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
2) Create the "oplsaa_subset.prm" file by making a copy of the "oplsaa.prm"
file, renaming it to "oplsaa_subset.prm", and deleting the atoms you don't need.
For example, if you are building a simple alkane chain, you would delete every
line beginning with the word "atom", except for these three lines:
atom 80 13 CT "Alkane CH3-" 6 12.011 4
atom 81 13 CT "Alkane -CH2-" 6 12.011 4
atom 85 46 HC "Alkane H-C" 1 1.008 1
(Leave the rest of the file unmodified.)
3) Create the "oplsaa.lt" file using this command:
oplsaa_moltemplate.py oplsaa_subset.prm
(Credit to Jasen Lambert for contributing this useful script.)
4) Create the "system.data", "system.in.init", and "system.in.settings"
files which LAMMPS will read by running:
moltemplate.sh system.lt
5)
To run LAMMPS, you must make sure LAMMPS was built with the "USER-MISC" package.
(because it uses dihedral_style fourier)
To do this, type "make yes-user-misc" before compiling LAMMPS.
http://lammps.sandia.gov/doc/Section_start.html#start_3
6) Run LAMMPS in this order:
lmp_g++ -i run.in.min
lmp_g++ -i run.in.npt
lmp_g++ -i run.in.nvt
(Replace "lmp_g++" with the name of the LAMMPS executable you are using.)
---- Details ----
The "Hexadecane" molecule, as well as the "CH2", and "CH3" monomers it contains
use the OPLSAA force-field. This means that when we define these molecules,
we only specify the atom names, bond list, and coordinates.
We do not have to list the atom charges, angles, dihedrals, or impropers.
The rules for creating atomic charge and angle topology are contained in
the "oplsaa.lt" file created by step 3) above. The "ch2group.lt",
"ch3group.lt", and "hexadecane.lt" files all refer to "oplsaa.lt",
(as well as the "OPLSAA" force-field object which it defines). Excerpt:
import "oplsaa.lt"
CH2 inherits OPLSAA { ...
CH3 inherits OPLSAA { ...
Hexadecane inherits OPLSAA { ...
Alternatively, you can manually define a list of angles, dihedrals, and
improper interactions in these files, instead of asking the force-field
to generate them for you. You can also specify some of the angles and
dihedrals explicitly, and let the force-field handle the rest.
(Many of the molecule examples which come with moltemplate do this.)
box at room temperature and atmospheric pressure. Please read "WARNING.TXT".
NOTE: This particular file contains instructions for how to build molecules
using the OPLSAA force-field. However, moltemplate is not limited to
OPLSAA. You can use other force-fields, or define your own force-fields
(or provide a list of bonded interactions explicitly).
-------- INSTRUCTIONS: ---------
1) Download the "oplsaa.prm" file containing the OPLS force field
parameters. I do not have permission to distribute those parameters,
but you can download them from one of these URLS:
http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm
http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm
2) Create the "oplsaa_subset.prm" file by making a copy of the "oplsaa.prm"
file, renaming it to "oplsaa_subset.prm", and deleting the atoms you don't need.
For example, if you are building a simple alkane chain, you would delete every
line beginning with the word "atom", except for these three lines:
atom 80 13 CT "Alkane CH3-" 6 12.011 4
atom 81 13 CT "Alkane -CH2-" 6 12.011 4
atom 85 46 HC "Alkane H-C" 1 1.008 1
(Leave the rest of the file unmodified.)
3) Create the "oplsaa.lt" file using this command:
oplsaa_moltemplate.py oplsaa_subset.prm
(Credit to Jasen Lambert for contributing this useful script.)
4) Create the "system.data", "system.in.init", and "system.in.settings"
files which LAMMPS will read by running:
moltemplate.sh system.lt
5)
To run LAMMPS, you must make sure LAMMPS was built with the "USER-MISC" package.
(because it uses dihedral_style fourier)
To do this, type "make yes-user-misc" before compiling LAMMPS.
http://lammps.sandia.gov/doc/Section_start.html#start_3
6) Run LAMMPS in this order:
lmp_g++ -i run.in.min
lmp_g++ -i run.in.npt
lmp_g++ -i run.in.nvt
(Replace "lmp_g++" with the name of the LAMMPS executable you are using.)
---- Details ----
The "Hexadecane" molecule, as well as the "CH2", and "CH3" monomers it contains
use the OPLSAA force-field. This means that when we define these molecules,
we only specify the atom names, bond list, and coordinates.
We do not have to list the atom charges, angles, dihedrals, or impropers.
The rules for creating atomic charge and angle topology are contained in
the "oplsaa.lt" file created by step 3) above. The "ch2group.lt",
"ch3group.lt", and "hexadecane.lt" files all refer to "oplsaa.lt",
(as well as the "OPLSAA" force-field object which it defines). Excerpt:
import "oplsaa.lt"
CH2 inherits OPLSAA { ...
CH3 inherits OPLSAA { ...
Hexadecane inherits OPLSAA { ...
Alternatively, you can manually define a list of angles, dihedrals, and
improper interactions in these files, instead of asking the force-field
to generate them for you. You can also specify some of the angles and
dihedrals explicitly, and let the force-field handle the rest.
(Many of the molecule examples which come with moltemplate do this.)
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