Layering of Resolutions

CGsmiles enables the representation of molecular graphs at arbitrary resolutions and their connection to progressively finer resolutions, allowing for the hierarchical layering of multiple levels of details.

Basic Syntax Features

Base Graph & Resolutions

The notation starts with the coarsest representation of the system – the base graph. This graph is enclosed in curly braces. Each additional resolution is represented as a list of fragment graphs, also enclosed in curly braces and separated from the preceding resolution graph by a period. If the final resolution graph is at the atomic level, either CGsmiles or OpenSMILES syntax can be used to describe the fragment graph. This dual approach allows seamless conversion to atomistic resolution using established standards, while also supporting intermediate coarse-grained representations.

{coarsest-graph}.{fragments-resolution-1}.{fragments-resolution-2}

Advanced Syntax Features

Linearizing Rings

Rings at the atomistic resolution can often be mapped into linear structures at the CG level, a common practice in chemically specific force fields such as Martini. In the CGsmiles notation, bond orders at the coarser resolution are utilized to describe such a case.

For example, cyclohexane is represented at the Martini 3 level with a bond order of 2. This indicates that at the next finer resolution level, two bonds must connect the atoms corresponding to the two CG nodes.

Martini3 Cyclohexane
{[#SC3]=[#SC3]}.{#SC3=[$]CCC[$]}

This approach also extends to more complex cases, such as splitting fused rings with three or more shared bonds at the CG level. Each additional ring increases the bond order.

Napthalene split as two particles
{[#A]#[#A]}.{#A=[$]CCC[$]CC[$]}

The current CGSimles syntax supports bond orders up to 4, which defines the maximum number of ring connections that can be represented linearly.

Virtual Edges

In certain scenarios, a CG model might include interacting particles that do not correspond to any finer-resolution nodes or atoms. For example, at the Martini 3 resolution glucose is represented by three CG particles splitting the sugar ring and one additional virtual particle. The TC4 bead captures the hydrophobic interactions at the ring center but lacks any corresponding fragments at finer resolution. To accommodate such particles, the CGsmiles notation employs zero bond order edges, referred to as virtual edges.

Martini 3 Glucose
{[#SP4r]1.2[#SP4r].3[#SP1r]1.[#TC4]23}.{#SP4r=OC[$]C[$]O,#SP1r=[$]OC[$]CO}

Virtual edges are ignored when establishing connections and any particle with only virtual edges is excluded entirely when transitioning to finer resolutions. We note that these virtual edges and virtual particles are not to be confused with the GROMACS virtual sites. A virtual site in GROMACS describes how a particle’s coordinates are constructed. If a virtual side describes real atoms or CG particles they would be treated as regular nodes rather than virtual ones.

Overloading Wildcards

In certain cases, a single CG graph might describe more than one molecule at the fine-grained resolution because of a loss in resolution at the CG level. An example are Martini lipids such as POPC. POPC can describe lipids with a tail length of 16 or 18 carbons and thus represents at least four molecules when accounting for the position for the double bond. To capture this feature CGsmiles allows to overload the wildcard (*) syntax using annotations. In OpenSMILES a wildcard means any atom can be placed at the wildcard position. To specify a selection of atoms CGsmiles allows to annotate a wildcard using the select keyword abbreviated as ‘s’. Thus, a tail bead in POPC could be written as C1=CCCC[*;s=C,0][*;s=C,0]. Note that the current molecule resolver is not able to handle wildcard overloading.