Scientific introduction

This page describes various important scientific considerations to keep in mind when working with NEXTMOL Modeling.

Basic concepts

The basic building block of a workflow in NEXTMOL Modeling is a molecule. Every molecule is composed by components, and each component is composed by atoms. For some applications, the concept of residue is also considered.

Components

The concept of molecule and component overlap in the majority of the applications. In fact, when a molecule is generated from the platform molecule designer, the new molecule is composed by one single component, and therefore the two concepts refer to the same entity. However, the platform also allows to upload files describing complex systems. In that case, the new system is considered as a single molecule from the point of view of the platform, but the various entities constituting the system are recognized and treated as separate components. The discriminant to distinguish one entity from one another is the potential: atoms within the same component experience a different potential compared to all the other atoms. In general, inter-component potentials are non-bonded interactions, while intra-component interactions are bonded interactions. Several operations in the platform allow to perform actions on particular components, selecting them by their name.

Importantly, component names are not unique within a system. For instance, replicas of an original component will all have the same name, and we implement checks to ensure that components with the same name always contain the same atom types. In other words, the concept of a component name in the platform is more akin to the idea of a molecule kind or type. If two or more different molecules with the same component names are present in a workflow, issues may arise during job execution. To address this, we implemented the option to rename components within a workflow: select the molecule in the workflow, click on 'EDIT STEP,' and you will find the rename option.

Except for the just described rename, the name of a component stays the same throughout the workflow.

Atoms

Atoms represent the smallest unit in a system. However, they do not always correspond to the physical atoms. They can represent a group of atoms in the united atom representation, or ghost atoms to add charge points in a system. Each atom has an atom type associated. Except for DFT application, the atom type does not necessarily correspond to the element of the atom; instead, it aligns with the atom type defined by the potential. For example, in MD applications there will be different atom types for different chemical environments. Each atom also has a name. Atoms names are not unique in the system, but can be visualized in the molecule visualizer.

Residues

Residues are groups of atoms within a component. They can be present or not, based on the application. They have an associated name that is not unique in a system.

System Operation Conventions

The system operations implemented in NEXTMOL Modeling offer a flexible way to construct simulation systems. The following details should be kept in mind:

  • The simulation cell is always orthorhombic, meaning the cell angles are always 90°.

  • Periodic boundary conditions (PBCs) are features that can be selected for some operations and are NOT a property of a particular system.

  • Systems are always treated as unwrapped system on a component basis, meaning atoms within a component will never be separated by PBC.

These decisions greatly simplify the treatment of several operations, allowing them to be performed seamlessly, regardless of whether PBC are applied or not. Operations where PBC are selected ensure that the geometric center of all components remains within the simulation cell.

When MD/DFT simulations are performed with PBC, the corresponding trajectories are saved in wrapped form. However, the post-processing functions will take care of unwrapping the trajectories as requested by the operation. Furthermore, when a system is extracted from a trajectory, the same conventions explained above are applied, ensuring consistency in the treatment of systems.

Technology in use

The term technology refers to the combination of the simulation method and code. For example, we might have technologies MD-gromacs, MD-lammps, DFT-PBE-CP2K and so on. The technology for a workflow is determined by the POTENTIAL selected for the first molecule added to the workflow. If, for instance, a gromacs MD potential is selected, the entire workflow will be labelled as a gromacs MD workflow, and only molecules with the corresponding available potential can be selected. The simulation will be Gromacs simulation. Only one technology can be used in a workflow.