In this example, we’ll build a gold nanoparticle and equilibrate it to a temperature of 300K. In future posts, we’ll add ligands and solvent to this structure. Here’s a sneak preview of the nanoparticle we’ll make here:
NP15_300K

  1. Start with an input .omd file for the metal of your choice. We’ll be creating gold.omd for this example.
    <OpenMD>
      <MetaData>
    molecule{
    name = "Au";

    atom[0]{
    type = "Au";
    position(0.0, 0.0, 0.0);
         }
    }

    component{
    type = "Au";
    nMol = 1;
    }

    forceField = "SC";
    forceFieldFileName = "SuttonChen.QSC.frc";
      </MetaData>
    </OpenMD>
  2. Now to build the nanoparticle. We’ll choose a radius of 15 Å and use the lattice constant of gold, 4.08 Å. We’ll call our initial structure NP15.omd.
    nanoparticleBuilder --latticeConstant=4.08 --radius=15 gold.omd -o NP15.omd
  3. To take a look at the structure we’ve just created, you can use the following command:
    Dump2XYZ -i NP15.omd

    to create a file called NP15.xyz, which can be viewed in VMD, Jmol, or any other chemical structure viewer.

  4. Add the following lines to the new NP15.omd file below the forceFieldFileName line. This sets some details for the simulation.
    ensemble = "LHull";
    targetTemp = 5;
    targetPressure = 1;
    viscosity = 0.1;
    dt = 4.0;
    runTime = 2E5;

    sampleTime = 2000.0;
    statusTime = 4;
    seed = 985456376;

    usePeriodicBoundaryConditions = "false";
    tauThermostat = 1E3;
    tauBarostat = 5E3;
  5. NanoparticleBuilder carves a nanoparticle of our chosen radius out of a perfect gold crystal. We need to give the atoms some initial velocities before we start equilibrating. We’ll start it out at 5K:
    thermalizer -t 5 NP15.omd -o NP15_5K.omd
  6. For the first step in the equilibration we need to let the gold lattice structurally relax. NP15_5K.omd can now be run:
    openmd NP15_5K.omd
  7. Running the simulation will create several new files. NP15_5K.dump contains the trajectory of the simulation. Statistics such as temperature, pressure, and energy will be recorded in the NP15_5K.stat file and can be viewed using:
    xmgrace -nxy NP15_5K.stat
  8. The end-of-run file NP15_5K.eor stores the last configuration of the simulation. We’ll copy it to a new .omd file.
    cp NP15_5K.eor NP15_100K.omd
  9. To continue with the equilibration we need to change the targetTemp of NP15_100K.omd. We’ll increase it to 100 and run the NP15_100K.omd file.
  10. We’ll continue the procedure of copying the .eor file to a new .omd file and increasing the temperature until we’ve reached 300K. Temperature increases of 50 – 100K and simulation times of 100 – 200 ps are reasonable.
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