Moltemplate Examples:

There are too many moltemplate examples to include here.

To get all the examples and documentation, please visit the download page.

(Please send new examples and force fields to )

Custom Force-Field Examples: here

Molecule Examples:

Water mixed with sodium & chloride ions (click below for input files)
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 (click below for input files)
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
 
Run Using:

 lmp_mpi -i run.in.nvt
 
Building a molecule ("butane") from smaller subunits using the COMPASS force field (click below for input files)
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
Build Using:

 moltemplate.sh system.lt
   
    (warnings and recommendtions...)
Run Using:
     
 lmp_mpi -i run.in.min
 lmp_mpi -i run.in.nvt
 
Building a simple polymer (using the OPLS force field) (click below for input files)
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.TXT
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) (click below for input files)
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) (click below for input files)
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 (Explicit LJ Solvent) (click below for input files)
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 (click below for input files)
Requirements: This example uses PACKMOL (For an alternative method, see system.lt )
MARTINI coarse-grained DPPC lipid MARTINI (2-body coarse grained) water model 13ns simulated with LAMMPS 13ns simulated with LAMMPS
README.TXT
lipid.lt
water.lt
system.lt
README_pm.txt
lipid.xyz
water.xyz
mix_lipids+water.inp
run.in.min
run.in.npt
run.in.nvt
(video)
Build Using:


 packmol < mix_lipids+water.inp 
 moltemplate.sh -xyz system.xyz system.lt
 
Run Using:

 lmp_mpi -i run.in.min
 lmp_mpi -i run.in.npt
 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. Click below for input files.)
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 click below for input files
Requirements: This example requires that LAMMPS is built with the optional USER-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
 
Multicomponent vesicle with protein inclusions click below for input files
Requirements: This example requires PACKMOL. LAMMPS must be built with the optional USER-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) multicomponent vesicle
Moltemplate files:
README_mt.txt,
CGLipidBr2005.lt,
table_int.dat,
1beadProtSci2010.lt,
system.lt
PACKMOL files:
README_pm.txt,
DPPC.xyz,
DLPC.xyz,
protein.xyz,
step1_proteins.inp,
step2_innerlayer.inp,
step3_outerlayer.inp

LAMMPS files:
run.in.min,
run.in.nvt

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

 packmol < step1_proteins.inp    # requires 20 minutes
 packmol < step2_innerlayer.inp  # at least 90 minutes
 packmol < step3_outerlayer.inp  # at least 4 hours (creates system.xyz)
 moltemplate.sh -xyz system.xyz system.lt
Run Using:

 lmp_mpi -i run.in.min
 lmp_mpi -i run.in.nvt
 
Ellipsoidal particles (Moltemplate can build systems containing ellipsoids and point-dipoles. Click below for input files)
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.txt
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