8.6.4. Moltemplate Tutorial — LAMMPS documentation

\(\renewcommand{\AA}{\text{Å}}\)

# 8.6.4. Moltemplate Tutorial

In this tutorial, we are going to use the tool Moltemplate from https://moltemplate.org/ to set up a classical molecular dynamic simulation using the OPLS-AA force field. The first task is to describe an organic compound and create a complete input deck for LAMMPS. The second task is to use moltemplate to build a polymer. The third task is to map the OPLS-AA force field to a molecular sample created with an external tool, e.g. PACKMOL, and exported as a PDB file. The files used in this tutorial can be found in the `tools/moltemplate/tutorial-files` folder of the LAMMPS source code distribution.

Many more examples can be found here: https://moltemplate.org/examples.html

## Simulating an organic solvent

This example aims to create a cubic box of the organic solvent formamide.

The first step is to create a molecular topology in the LAMMPS-template (LT) file format representing a single molecule, which will be stored in a Moltemplate object called `_FAM inherits OPLSAA {}`. This command states that the object `_FAM` is based on an existing object called `OPLSAA`, which contains OPLS-AA parameters, atom type definitions, partial charges, masses and bond-angle rules for many organic and biological compounds. The atomic structure is the starting point to populate the command `write('Data Atoms') {}`, which will write the `Atoms` section in the LAMMPS data file. The OPLS-AA force field uses the `atom_style full`, therefore, this column format is used: `# atomID molID atomType charge coordX coordY coordZ`. The `atomID`s are replaced with Moltemplate `$`-type variables, which are then substituted with unique numerical IDs. The same logic is applied to the `molID`, except that the same variable is used for the whole molecule. The atom types are assigned using `@`-type variables. The assignment of atom types (e.g. `@atom:177`, `@atom:178`) is done using the OPLS-AA atom types defined in the “In Charges” section of the file `oplsaa2024.lt`, looking for a reasonable match with the description of the atom. The resulting file (`formamide.lt`) follows:

    import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt  # defines OPLSAA

    _FAM inherits OPLSAA {

      # atomID    molID  atomType  charge  coordX  coordY  coordZ
      write('Data Atoms') {
        $atom:C00  $mol  @atom:235  0.00    0.100   0.490   0.0
        $atom:O01  $mol  @atom:236  0.00    1.091  -0.250   0.0
        $atom:N02  $mol  @atom:237  0.00   -1.121  -0.181   0.0
        $atom:H03  $mol  @atom:240  0.00   -2.013   0.272   0.0
        $atom:H04  $mol  @atom:240  0.00   -1.056  -1.190   0.0
        $atom:H05  $mol  @atom:279  0.00    0.144   1.570   0.0
      }

      # A list of the bonds in the molecule:
      # BondID   AtomID1   AtomID2
      write('Data Bond List') {
        $bond:C1 $atom:C00 $atom:O01
        $bond:C2 $atom:C00 $atom:H05
        $bond:C3 $atom:C00 $atom:N02
        $bond:C4 $atom:N02 $atom:H03
        $bond:C5 $atom:N02 $atom:H04
      }
    }

You don’t have to specify the charge in this example because the OPLSAA force-field assigns charge according to the atom type. (This is not true when using other force fields.) A “Data Bond List” section is needed as the atom type will determine the bond type. The other bonded interactions (e.g. angles, dihedrals, and impropers) will be automatically generated by Moltemplate.

If the simulation is not charge-neutral, or Moltemplate complains that you have missing bond, angle, or dihedral types, this probably means that at least one of your atom types is incorrect (or that perhaps there is no suitable atom type currently defined in the `oplsaa2024.lt` file).

The second step is to create a master file with instructions to build a starting structure and the LAMMPS commands to run an NPT simulation. The master file (`solv_01.lt`) follows:

    import formamide.lt  # Defines "_FAM" and OPLSAA

    # Distribute the molecules on a 5x5x5 cubic grid with spacing 4.6
    solv = new _FAM [5].move( 4.6, 0, 0)
                    [5].move( 0, 4.6, 0)
                    [5].move( 0, 0, 4.6)
    solv[*][*][*].move(-11.5, -11.5, -11.5)

    # Set the simulation box.
    write_once("Data Boundary") {
     -11.5 11.5 xlo xhi
     -11.5 11.5 ylo yhi
     -11.5 11.5 zlo zhi
    }

    # Note: The lines below in the "In Run" section are often omitted.

    write_once("In Run"){
     # Create an input deck for LAMMPS.
     # Run an NPT simulation.
     # Input variables.
     variable run    string solv_01   # output name
     variable ts     equal  1         # timestep
     variable temp   equal  300       # equilibrium temperature
     variable p      equal  1.        # equilibrium pressure
     variable d      equal  1000      # output frequency
     variable equi   equal  5000      # Equilibration steps
     variable prod   equal  30000     # Production steps

     # Derived variables.
     variable tcouple equal \$\{ts\}*100
     variable pcouple equal \$\{ts\}*1000

     # Output.
     thermo          \$d
     thermo_style custom step etotal evdwl ecoul elong ebond eangle &
     edihed eimp ke pe temp press vol density cpu
     thermo_modify flush yes

     # Trajectory.
     dump TRJ all dcd \$d \$\{run\}.dcd
     dump_modify TRJ unwrap yes

     # Thermalisation and relaxation, NPT ensemble.
     timestep       \$\{ts\}
     fix             NPT all npt temp \$\{temp\} \$\{temp\} \$\{tcouple\} iso \$p \$p \$\{pcouple\}
     velocity all create \$\{temp\} 858096 dist gaussian
     # Short runs to update the PPPM settings as the box shinks.
     run    \$\{equi\} post no
     run    \$\{equi\} post no
     run    \$\{equi\} post no
     run    \$\{equi\}
     # From now on, the density shouldn't change too much.
     run    \$\{prod\}
     unfix NPT
    }

The first two commands insert the content of files `oplsaa2024.lt` and `formamide.lt` into the master file. At this point, we can use the command `solv = new _FAM [N]` to create N copies of a molecule of type `_FAM`. In this case, we create an array of 5*5*5 molecules on a cubic grid using the coordinate transformation command `.move( 4.6, 0, 0)`. See the Moltemplate documentation to learn more about the syntax. As the sample was created from scratch, we also specify the simulation box size in the “Data Boundary” section.

The LAMMPS setting for the force field are specified in the file `oplsaa2024.lt` and are written automatically in the input deck. We also specify the boundary conditions and a set of variables in the “In Init” section.

The remaining commands to run an NPT simulation are written in the “In Run” section. Note that in this script, LAMMPS variables are protected with the escape character `\` to distinguish them from Moltemplate variables, e.g. `\$\{run\}` is a LAMMPS variable that is written in the input deck as `${run}`.

(Note: Moltemplate can be slow to run, so you need to change you run settings frequently, I recommended moving those commands (from “In Run”) out of your .lt files and into a separate file. Moltemplate creates a file named `run.in.EXAMPLE` for this purpose. You can put your run settings and fixes that file and then invoke LAMMPS using `mpirun -np 4 lmp -in run.in.EXAMPLE` instead.)

Compile the master file with:

    moltemplate.sh solv_01.lt
    cleanup_moltemplate.sh   # <-- optional: see below

(Note: The optional “cleanup_moltemplate.sh” command deletes unused atom types, which sometimes makes LAMMPS run faster. But it does not work with many-body pair styles or dreiding-style h-bonds. Fortunately most force fields, including OPLSAA, don’t use those features.)

Then execute the simulation with the following:

    mpirun -np 4 lmp -in solv_01.in -l solv_01.log

Snapshot of the sample at the beginning and end of the simulation. Rendered with Ovito.

## Building a simple polymer

Moltemplate is particularly useful for building polymers (and other molecules with sub-units). As an simple example, consider butane:

The `butane.lt` file below defines Butane as a polymer containing 4 monomers (of type `CH3`, `CH2`, `CH2`, `CH3`).

    import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt  # defines OPLSAA

    CH3 inherits OPLSAA {

      # atomID    molID   atomType  charge   coordX   coordY    coordZ
      write("Data Atoms") {
        $atom:c  $mol:... @atom:54   0.0   0.000000  0.4431163  0.000000
        $atom:h1 $mol:... @atom:60   0.0   0.000000  1.0741603  0.892431
        $atom:h2 $mol:... @atom:60   0.0   0.000000  1.0741603 -0.892431
        $atom:h3 $mol:... @atom:60   0.0  -0.892431 -0.1879277  0.000000
      }
      # (Using "$mol:..." indicates this object ("CH3") is part of a larger
      #  molecule. Moltemplate will share the molecule-ID with that molecule.)

      # A list of the bonds within the "CH3" molecular sub-unit:
      # BondID   AtomID1   AtomID2
      write('Data Bond List') {
        $bond:ch1 $atom:c $atom:h1
        $bond:ch2 $atom:c $atom:h2
        $bond:ch3 $atom:c $atom:h3
      }
    }

    CH2 inherits OPLSAA {

      # atomID    molID   atomType  charge   coordX   coordY    coordZ
      write("Data Atoms") {
        $atom:c  $mol:... @atom:57   0.0   0.000000  0.4431163  0.000000
        $atom:h1 $mol:... @atom:60   0.0   0.000000  1.0741603  0.892431
        $atom:h2 $mol:... @atom:60   0.0   0.000000  1.0741603 -0.892431
      }

      # A list of the bonds within the "CH2" molecular sub-unit:
      # BondID   AtomID1   AtomID2
      write('Data Bond List') {
        $bond:ch1 $atom:c $atom:h1
        $bond:ch2 $atom:c $atom:h2
      }
    }

    Butane inherits OPLSAA {

      create_var {$mol}  # optional:force all monomers to share the same molecule-ID

      # - Create 4 monomers
      # - Move them along the X axis using ".move()",
      # - Rotate them 180 degrees with respect to the previous monomer
      monomer1 = new CH3
      monomer2 = new CH2.rot(180,1,0,0).move(1.2533223,0,0)
      monomer3 = new CH2.move(2.5066446,0,0)
      monomer4 = new CH3.rot(180,0,0,1).move(3.7599669,0,0)

      # A list of the bonds connecting different monomers together:
      write('Data Bond List') {
        $bond:b1  $atom:monomer1/c $atom:monomer2/c
        $bond:b2  $atom:monomer2/c $atom:monomer3/c
        $bond:b3  $atom:monomer3/c $atom:monomer4/c
      }
    }

Again, you don’t have to specify the charge in this example because OPLSAA assigns charges according to the atom type.

This `Butane` object is a molecule which can be used anywhere other molecules can be used. (You can arrange `Butane` molecules on a lattice, as we did previously. You can also modify individual butane molecules by adding or deleting atoms or bonds. You can add bonds between specific butane molecules or use `Butane` as a sub-unit to define even larger molecules. See the moltemplate manual for details.)

## How to build a complex polymer

A similar procedure can be used to create more complicated polymers, such as the NIPAM polymer example shown below. For details, see:

https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_OPLSAA/NIPAM_polymer+water+ions

## Mapping an existing structure

Another helpful way to use Moltemplate is mapping an existing molecular sample to a force field. This is useful when a complex sample is assembled from different simulations or created with specialized software (e.g. PACKMOL). (Note: The previous link shows how to build this entire system from scratch using only moltemplate. However here we will assume instead that we obtained a PDB file for this system using PACKMOL.)

As in the previous examples, all molecular species in the sample are defined using single-molecule Moltemplate objects. For this example, we use a short polymer in a box containing water molecules and ions in the PDB file `model.pdb`.

It is essential to understand that the order of atoms in the PDB file and in the Moltemplate master script must match, as we are using the coordinates from the PDB file in the order they appear. The order of atoms and molecules in the PDB file provided is as follows:

- 500 water molecules, with atoms ordered in this sequence:

      ATOM      1  O   MOL D   1       5.901   7.384   1.103  0.00  0.00      DUM
      ATOM      2  H   MOL D   1       6.047   8.238   0.581  0.00  0.00      DUM
      ATOM      3  H   MOL D   1       6.188   7.533   2.057  0.00  0.00      DUM

- 1 polymer molecule.

- 1 Ca2+ ion.

- 2 Cl- ions.

In the master LT file, this sequence of molecules is matched with the following commands:

    # Create the sample.
    wat=new SPC[500]
    pol=new PolyNIPAM[1]
    cat=new Ca[1]
    ani=new Cl[2]

Note that the first command would create 500 water molecules in the same position in space, and the other commands will use the coordinates specified in the corresponding molecular topology block. However, the coordinates will be overwritten by rendering an external atomic structure file. Note that if the same molecule species are scattered in the input structure, it is recommended to reorder and group together for molecule types to facilitate the creation of the input sample.

The molecular topology for the polymer is created as in the previous example, with the atom types assigned as in the following schema:

Atom types assigned to the polymer’s repeating unit.

The molecular topology of the water and ions is stated directly into the master file for the sake of space, but they could also be written in a separate file(s) and imported before the sample is created.

The resulting master LT file defining short annealing at a fixed volume (NVT) follows:

    # Use the OPLS-AA force field for all species.
    import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt
    import PolyNIPAM.lt

    # Define the SPC water and ions as in the OPLS-AA
    Ca inherits OPLSAA {
      write("Data Atoms"){
        $atom:a1  $mol:. @atom:412 0.0  0.00000 0.00000 0.000000
      }
    }
    Cl inherits OPLSAA {
      write("Data Atoms"){
        $atom:a1  $mol:. @atom:401 0.0  0.00000 0.00000 0.000000
      }
    }
    SPC inherits OPLSAA {
      write("Data Atoms"){
        $atom:O  $mol:. @atom:9991 0.  0.0000000 0.00000 0.0000000
        $atom:H1 $mol:. @atom:9990 0.  0.8164904 0.00000 0.5773590
        $atom:H2 $mol:. @atom:9990 0. -0.8164904 0.00000 0.5773590
      }
      write("Data Bond List") {
        $bond:OH1 $atom:O $atom:H1
        $bond:OH2 $atom:O $atom:H2
      }
    }

    # Create the sample.
    wat=new SPC[500]
    pol=new PolyNIPAM[1]
    cat=new Ca[1]
    ani=new Cl[2]

    # Periodic boundary conditions:
    write_once("Data Boundary"){
      0 26 xlo xhi
      0 26 ylo yhi
      0 26 zlo zhi
    }

    write_once("In Init"){
      boundary p p p  # "p p p" is the default. This line is optional.
      neighbor 3 bin  # (This line is also optional in this example.)
    }

    # Note: The lines below in the "In Run" section are often omitted.

    # Run an NVT simulation.
    write_once("In Run"){
      # Input variables.
      variable run    string sample01  # output name
      variable ts     equal  2         # timestep
      variable temp   equal  298.15    # equilibrium temperature
      variable p      equal  1.        # equilibrium pressure
      variable equi   equal  30000     # equilibration steps

      # Set the output.
      thermo          1000
      thermo_style    custom step etotal evdwl ecoul elong ebond eangle &
      edihed eimp pe ke temp press atoms vol density cpu
      thermo_modify flush yes
      compute pe1 all pe/atom pair
      dump TRJ all custom 100 \$\{run\}.dump id xu yu zu c_pe1

      # Minimise the input structure, just in case.
      minimize        .01 .001 1000 100000
      write_data \$\{run\}.min

      # Set the constrains.
      group watergroup type @atom:9991 @atom:9990
      fix 0 watergroup shake 0.0001 10 0 b @bond:spcO_spcH a @angle:spcH_spcO_spcH

      # Short annealing.
      timestep        \$\{ts\}
      fix       1 all nvt temp \$\{temp\} \$\{temp\} \$(100*dt)
      velocity    all create \$\{temp\} 315443
      run             \$\{equi\}
      unfix 1
    }

In this example, the water model is SPC and it is defined in the `oplsaa2024.lt` file with atom types `@atom:9991` and `@atom:9990`. For water we also use the `group` and `fix shake` commands with Moltemplate `@`-type variables, to ensure consistency with the numerical values assigned during compilation. To identify the bond and angle types, look for the extended `@atom` IDs, which in this case are:

    replace{ @atom:9991 @atom:9991_bspcO_aspcO_dspcO_ispcO }
    replace{ @atom:9990 @atom:9990_bspcH_aspcH_dspcH_ispcH }

From which we can identify the following “Data Bonds By Type”: `@bond:spcO_spcH @atom:*_bspcO*_a*_d*_i* @atom:*_bspcH*_a*_d*_i*` and “Data Angles By Type”: `@angle:spcH_spcO_spcH @atom:*_b*_aspcH*_d*_i* @atom:*_b*_aspcO*_d*_i* @atom:*_b*_aspcH*_d*_i*`

Compile the master file with:

    moltemplate.sh -pdb model.pdb sample01.lt
    cleanup_moltemplate.sh

And execute the simulation with the following:

    mpirun -np 4 lmp -in sample01.in -l sample01.log

Sample visualized with Ovito loading the trajectory into the DATA file written after minimization.

(OPLS-AA) Jorgensen, W.L., Ghahremanpour, M.M., Saar, A., Tirado-Rives, J., J. Phys. Chem. B, 128(1), 250-262 (2024).

(Moltemplate) Jewett et al., J. Mol. Biol., 433(11), 166841 (2021)