Moltemplate Examples:

Some examples are missing from this list.

(To get all the examples, download moltemplate from the moltemplate web page. They are included in the download, along with extra README files and other documentation.)

Custom Force-Fields

To create your own force fields, see these examples.

(Please send new examples and force fields to )

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
 
Coarse-grained lipid bilayer (using the MARTINI force field) (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
 
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
system.lt,
run.in.npt, (video)
Build Using:

 moltemplate.sh system.lt
 
Run Using:

 lmp_mpi -i run.in.npt
 
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
 
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
 
Aggregation of Simple Toy Heteropolymers (click below for input files)
monomer with a hydrophobic sidechain bead monomer with a hydrophilic sidechain bead a short polymer many short polymers
aggregation
monomer_H.lt
monomer_P.lt
forcefield.lt
polymer.lt system.lt run.in.nvt
Build Using:

 moltemplate.sh system.lt
 
Run Using:

 lmp_mpi -i run.in.nvt