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:
- Start with an input .md file for the metal of your choice. We’ll be creating gold.md for this example.
name = "Au";
type = "Au";
position(0.0, 0.0, 0.0);
type = "Au";
nMol = 1;
forceField = "SC";
forceFieldFileName = "SuttonChen.QSC.frc";
- 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.md.
nanoparticleBuilder --latticeConstant=4.08 --radius=15 gold.md -o NP15.md
- To take a look at the structure we’ve just created, you can use the following command:
Dump2XYZ -i NP15.md
- Add the following lines to the new NP15.md 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;
- 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.md -o NP15_5K.md
- For the first step in the equilibration we need to let the gold lattice structurally relax. NP15_5K.md can now be run:
- 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
- The end-of-run file NP15_5K.eor stores the last configuration of the simulation. We’ll copy it to a new .md file.
cp NP15_5K.eor NP15_100K.md
- To continue with the equilibration we need to change the targetTemp of NP15_100K.md. We’ll increase it to 100 and run the NP15_100K.md file.
- We’ll continue the procedure of copying the .eor file to a new .md file and increasing the temperature until we’ve reached 300K. Temperature increases of 50 – 100K and simulation times of 100 – 200 ps are reasonable.