The Nano-to-Meso workflow

Summary

The aim of the Nano-to Meso Morphology workflow is to create structural models of pristine and doped organic semiconductors composed of about 106 molecules, using three distinct WaNos. Two levels of theory are used to describe the molecules: an all-atom (AA) force field and a coarse-grained (CG) force field. The workflow begins with the generation of an amorphous thin-film with the DEPOSIT WaNo. The molecules are described with an additive AA force field, which is used to deposit molecules sequentially on top of a fictitious potential wall, effectively growing an amorphous film of the desired material(s). A Monte-Carlo acceptance criterion is used to select the best adsorption sites during the growth of the film. The second WaNo, AAMD, is used to carry out a classical all-atom MD simulation in which the thin-film obtained from the previous WaNo is annealed at constant pressure. In addition, 3D periodic boundary conditions are enforced in order to turn the film into a bulk-like amorphous solid, which is used by the next WaNo to create a supercell of the desired size. At this stage, the MD simulation is carried out with the same AA force field used in the previous WaNo.

The third WaNo, CGMD, is designed to handle the creation and the dynamical evolution of mesoscopic samples, i.e. systems with a number of molecules of the order of 106 and box vectors of about one micron. The molecular constituents are described with a CG force field, in which groups of atoms are represented as a single particle with an ellipsoidal shape. The particles in the CG force field interact via an anisotropic attractive-repulsive Gay-Berne (GB) potential, plus electrostatic interactions. A molecule is then represented as a multi-site GB in a way that resembles in shape and interactions the atomistic models.

The tasks carried out by the CGMD WaNo are then to convert an atomistic model into a CG one, to up-scale the model by creating a supercell and finally to carry out a MD simulation. To date, the CGMD WaNo offers the possibility to carry out two types of MD simulations: the “Quick Amorphization” is used to stir a supercell with a cycle where the simulation box is expanded by a certain amount and then shrunk back to the initial volume. This sequence is designed to decrease the density of the sample and to create a new morphology for the supercell, which effectively removes the spurious periodicity of the initial supercell. A task called “Annealing” is instead used to carry out a classical MD simulation at constant volume or pressure. In both cases, the actual MD simulations are carried out with a modified version of the open-source program LAMMPS, which includes a new routine for the evaluation of electrostatic interactions for an arbitrary distribution of charges decorating the multi-site GB.

The AAMD and CGMD WaNos will create the relevant input files to run the MD simulations, while the user is expected to choose physical parameters such as the duration of the simulation, temperature and pressure, as well as the components of the studied system. The complete workflow is shown below.

Overview of the Nano-to-Meso workflow. An initial nano-scale morphology is generated in Deposit and passed to a classical all-atom MD simulation. The resulting x,y,z periodic morphology is expanded in a coarse-grained Molecular dynamics simulation in CGMD.

Tutorial: Creation of a mesoscopic sample of amorphous α-NPD from a thin-film model.

In this tutorial, a morphology of α-NPD molecules will be deposited using Deposit and expanded using AA and CGMD.

  • Deposit: Load the structure of a single α-NPD molecule in PDB format and the corresponding force field definition in the SPF format into the Deposit WaNo. Select the number of molecules to be deposited, the size of the simulation box and the simulation temperature.
  • AAMD: Select the directory containing the (gzipped) PDB files deposited with the previous WaNo. Load the force field in the CHARMM format (i.e. a topology and a parameter file, in the RTF and PRM format, respectively) and specify the same box size used previously. Select the “Film2Bulk” task, which will automatically convert the input morphology in a format suitable to run a MD simulation.
  • CGMD: Load the structure of a bulk-like amorphous sample in PDB format, along with the definition of the CG force field (i.e. a topology and a parameter file, in GBT and GBP format, respectively). Select the number of repeating units to make the supercell, in this case 10x10x10, the total number of steps, 500’000, corresponding to 10 ns of simulation, and select the task “Quick Amorphization”.

Overview of the mesoscopic package workflow, from a single molecule of α-NPD to a mesoscopic sample containing one million molecules.

Parameter explanations of the Nano-to-Meso Morphology Workflow

Deposit

Molecules

Click the + button to create another set of input fields for multiple input molecules

  • Molecule [PDB] PDB structure of the molecule to be deposited.
  • Forcefield [SPF] Forcefield file of the molecule to be deposited.
  • Mixing Ratio Ratio of the specified molecule. Ignored, if only one molecule is specified.

Simulation Parameters

  • Simulation Box [Lx,Ly,Lz] Half box size of the (optionally) x-y periodic simulation box.
  • PBC, PBC Cutoff [Å] Explicit PBC images are created inside a shell of size PBC Cutoff around the simulation box, if enabled.
  • Number of Molecules Number of molecules to be deposited.
  • Initial / Final Temperature [K] Every simulated annealing cycle starts at Initial Temperature and ends at Final Temperature using a geometric cooling schedule. Initial Temperature should be chosen higher than physical to allow for faster deposition.
  • SA Acc Temp [K] After each simulated annealing step the new conformation is accepted using this temperature.
  • Number of Steps Every simulated annealing cycle simulates for Number of Steps MC steps.
  • Number of SA cycles Number of SA cycles simulated annealing cycles are carried out. In case more than 1 CPU is allocated for the Deposit simulation SA cycles are carried out in parallel.

AAMD

  • Task Type of MD simulation to be carried out.
  • Force Field Topology and parameter files, in CHARMM format.
  • Deposit Film Directory Path to the directory containing the PDB files corresponding to the deposited film.
  • Restart If the simulation is restarted (as for a repeated annealing), select a restart file in LAMMPS format.
  • Components Number of components of the system. For each component, the corresponding name of Residue must be provided.
  • Simulation Box (Å) Vectors of the orthogonal simulation box.
  • Timestep (fs) Typical value: 2.0 fs. Use a smaller timestep if the system becomes unstable.
  • Duration (steps) Number of steps to be computed. The simulated time, in nanoseconds, will be: duration*timestep/1e6.
  • Frequency of Dumps (steps) The number of steps between saved configurations in the trajectory and the frequency at which thermodynamic properties (Energy, pressure, Volume) are computed and displayed.
  • Temperature (K) The initial and final temperature during a single run.
  • Pressure (atm) The initial and final pressure during a single run.
  • Damping constant (fs) Damping constant of the thermostat and barostat. Usually, the damping constant for the pressure should be higher than that for the temperature.
  • Number of CPUs Self-explanatory.

CGMD

  • Task Type of MD simulation to be carried out.
  • System A single PDB file containing an all-atom sample. If provided, this structure is converted into a coarse-grained representation.
  • Restart If the simulation is restarted (as for a repeated annealing), select a restart file in LAMMPS format.
  • Force Field Topology and parameter files, in GBT and GBP format.
  • Supercell If the input system is atomistic, then the simulated sample will be upscaled to the number of replicae specified here.
  • Timestep (fs) Typical value: 20.0 fs. Use a smaller timestep if the system becomes unstable.
  • Duration (steps) Number of steps to be computed. The simulated time, in nanoseconds, will be: duration*timestep/1e6.
  • Frequency of Dumps (steps) The number of steps between saved configurations in the trajectory and the frequency at which thermodynamic properties (Energy, pressure, Volume) are computed and displayed.
  • Temperature (K) The initial and final temperature during a single run.
  • Pressure (atm) The initial and final pressure during a single run.
  • Damping constant (fs) Damping constant of the thermostat and barostat. Usually, the damping constant for the pressure should be higher than that for the temperature.
  • Number of CPUs Self-explanatory.

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