Moltemplate Examples:

(Note: There are too many moltemplate examples to include here.

To get all the examples and documentation, click here.)


Custom Force-Field Examples: here

Molecule Examples:

Water mixed with sodium & chloride ions (README)
water (using the SPC/E model) sodium ion (single particle) chloride ion (single particle) initial configuration 100 ps after pressure equilibration (LAMMPS simulation)
spce.lt (water model) ions.lt system.lt run.in.npt
Build Using: 

 moltemplate.sh system.lt
Run Using: 

 lmp_mpi -i run.in.npt
Mixture of two small organic molecules using the OPLSAA force field (README)
ethylene benzene initial configuration
during pressure equilibration (LAMMPS simulation)
ethylene.lt
oplsaa.lt 		benzene.lt system.lt run.in.npt
Build Using: 

 moltemplate.sh system.lt
    (warnings and recommendtions...)
Run Using: 

 lmp_mpi -i run.in.nvt
Building a molecule ("butane") from smaller subunits using the COMPASS force field (README)
CH2 group CH2 group butane a box of butane molecules during pressure equilibration (LAMMPS simulation)
ch2group.lt
ch3group.lt
compass_published.lt 		butane.lt system.lt run.in.npt
run.in.nvt
Build Using: 

 moltemplate.sh system.lt
    (warnings and recommendtions...)
Run Using: 
 lmp_mpi -i run.in.npt
 lmp_mpi -i run.in.nvt
Building a simple polymer (using the OPLS force field) (README)
CH2 group CH2 group a simple polymer in a vacuum 1ns alkane chain in a vacuum. simulated with LAMMPS
ch3group.lt ch2group.lt alkane50.lt
system.lt
(Note: more complex shapes are possible) 		README.md
run.in.min
run.in.nvt
Build Using: 

 moltemplate.sh system.lt
    (warnings and recommendtions...)
Run Using: 
     
 lmp_mpi -i run.in.min
 lmp_mpi -i run.in.nvt
Carbon-Nanotube capillary (all-atom, explicit water) (README)
unit cell for building graphene and nanotubes two graphene walls connected by a carbon nanotube (reader's comment: atoms near junction should be adjusted. Chiral nanotubes need special treatment.) rhombohedron of water combined system with periodic boundaries .... wetting after 300ps
graphene.lt
nanotube.lt,
graphene_walls.lt 		spce.lt,
water_box.lt 		system.lt,
run.in.nvt,   (video)
Build Using: 

 moltemplate.sh system.lt
Run Using: 

 lmp_mpi -i run.in.nvt
Aggregation of Simple Toy Polymers (coarse grained)
monomer (contains 2 CG atoms) a short polymer

(Note: more complex shapes are possible) 		many short polymers 5x10^6 steps aggregation simulated using LAMMPS
monomer.lt
forcefield.lt 		polymer.lt system.lt run.in.nvt
Build Using: 

 moltemplate.sh -atomstyle "full" system.lt
Run Using: 
   lmp_mpi -i run.in.nvt
Translocation of a short polymer through a pore in explicit LJ solvent (README)
Requirements: This example requires that LAMMPS is built with the optional RIGID package.
solvent (holes carved out for solutes) two walls (one with hole) short polymer complete system (solvent shrunk for ease of viewing)
solvent_single.lt,
solvent.lt 		wall_single.lt,
walls.lt 		monomer.lt,
polymer.lt,
polymer_forcefield.lt 		system.lt,
run.in.npt,   (video)
Build Using: 

 moltemplate.sh system.lt
Run Using: 

 lmp_mpi -i run.in.npt
Coarse-grained lipid bilayer using the MARTINI force field and PACKMOL (README)
Requirements: This example uses PACKMOL (For an alternative method, see this example.)
MARTINI coarse-grained DPPC lipid MARTINI (2-body coarse grained) water model 13ns simulated with LAMMPS 13ns simulated with LAMMPS
README.md
DPPC.lt
water.lt
system.lt
martini.lt
README_packmol.txt
README_moltemplate.sh
DPPC.xyz
water.xyz
mix_lipids+water.inp
run.in.min
run.in.anneal
run.in.nvt 		(video)
Build Using: 


 packmol < mix_lipids+water.inp            # (create the "system.xyz" file)
 moltemplate.sh -xyz system.xyz system.lt
Run Using: 

 lmp_mpi -i run.in.min
 lmp_mpi -i run.in.anneal
 lmp_mpi -i run.in.nvt
Many-Body force field example: mW solvent + CG hydrocarbon mixture (Many-body force fields can be combined with ordinary, pairwise-additive force fields. README.)
Requirements: This example requires that LAMMPS is built with the MANYBODY package.
mW water solvent (single particle) cyclododecane (before minimization) initial configuration 400 ps phase separation & pressure equilibration (LAMMPS simulation)
README.png
watmw.lt 		cyclododecane.lt,
trappe1998.lt 		README.TXT
system.lt 		run.in.npt   (video)
Build Using: 

 moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt
Run Using: 

 lmp_mpi -i run.in.npt
Coarse-grained membrane protein (README)
Requirements: This example requires that LAMMPS is built with the optional MISC package, before additional code is added (in that order)
coarse-grained DPPC lipid coarse-grained DLPC lipid coarse-grained protein (hydrophilic beads face inwards) initial configuration (periodic boundaries not shown) 3ns periodic boundaries and pressure equilibration
CGLipidBr2005.lt,
table_int.dat 		1beadProtSci2010.lt,
system.lt run.in.npt
Build Using: 

 moltemplate.sh system.lt
Run Using: 

 lmp_mpi -i run.in.npt
Vesicle with protein inclusions (README)
Requirements: This example requires PACKMOL. LAMMPS must be built with the optional MISC package, before additional code is added (in that order)
coarse-grained DPPC lipid coarse-grained protein (hydrophilic beads face inwards) vesicle with proteins
Moltemplate files:
README
CGLipidBr2005.lt
table_int.dat
1beadProtSci2010.lt
system.lt 		PACKMOL files:
README_pm
DPPC.xyz
protein.xyz
step1_proteins.inp
step2_innerlayer.inp
step3_outerlayer.inp
LAMMPS files:
run.in.min
run.in.make_uniform
run_T=345K.in

This is a complex example requiring hours or days to set up. Please follow the instructions in the README files.
Build Using: 

 packmol < step1_proteins.inp    # requires ~40 minutes
 packmol < step2_innerlayer.inp  # requires ~10 hours
 packmol < step3_outerlayer.inp  # requires 1-3 days (creates "system.xyz" file)
 moltemplate.sh -xyz system.xyz system.lt
Run Using: 

 lmp_mpi -i run.in.min
 lmp_mpi -i run.in.make_uniform
 lmp_mpi -i run_T=345K.in
DNA polymer that follows a curve (README.md)
WARNING: To create an equilibrium polymer melt, you must use a "soft" potential to allow the polymer(s) to fully relax.
Requirements: This example requires that LAMMPS is built with the optional MISC package.
initial conformation with user-specified rotations after pressure equilibration (LAMMPS simulation) LAMMPS after confinement and initial relaxation
README.md
dna_monomer.lt dna_forcefield.lt 		curve_smooth.txt
(generated by ndmansfield and interpolate_curve.py ) 		dna_polymer.lt
(generated by genpoly_lt.py See below.) 		wall_particle.lt
wall.lt
system.lt
run.in.min
Build Using: 
  NMONOMERS=3058;           # number of monomers
  B=0.996                   # length per monomer
  Nx=11; Ny=11; Nz=11       # number of lattice sites

  # Generate a lattice polymer shape (integer coordinates)
  # Note: You must download "ndmansfield" at https://github.com/jewettaij/ndmansfield
  ./ndmansfield -box $Nx $Ny $Nz -seed 0 -tstart 1 -tsave 1000000 -tstop 1000000 > curve_lattice.txt

  # Interpolate and rescale the coordinates:
  SCALE=`echo "($NMONOMERS*$B)/($Nx*$Ny*$Nz-1)" | bc -l`   #physical curve length / #lattice sites
  interpolate_curve.py $NMONOMERS $SCALE < curve_lattice.txt > curve_smooth.txt

  # Create a moltemplate file ("dna_polymer.lt") for a polymer with this shape
  genpoly_lt.py -helix 102.7797 \
                -polymer-name 'DNAPolymer' \
                -monomer-name 'DNAMonomer' \
                -inherits 'DNAForceField' \
                -header 'import "dna_monomer.lt"' \
                -bond Backbone a a \
                -bond Backbone b b \
                -dihedral MajorGroove b b a a 0 1 1 2 \
                -dihedral Torsion a a b b 1 0 0 1 \
                -padding 20,20,20 \
                < curve_smooth.txt > dna_polymer.lt

  # (Note: The "system.lt" file contains a link to "dna_polymer.lt".)
  # Now run moltemplate to convert "system.lt" into LAMMPS format.
  moltemplate.sh system.lt
Run Using: 

 lmp_mpi -i run.in.min  #relax the polymer conformation
Ellipsoidal particles (Moltemplate can build systems containing ellipsoids and point-dipoles. README.md)
Requirements: This example requires that LAMMPS is built with the optional ASPHERE package.
initial conformation with user-specified rotations after pressure equilibration (LAMMPS simulation)
README.md
benzene_cg.lt 		system.lt run.in
Build Using: 
  moltemplate.sh -atomstyle "atomid atomtype flag density x y z" system.lt
                 -allow-wildcards -nocheck
Run Using: 

 lmp_mpi -i run.in