Coarse-Grained Modeling Workflow

The general workflow for a coarse-grained modeling project involves several steps. For some steps, the detailed workflow may depend on the model type or the potentials used. Links to the topics that describe the panels used or details of specific tasks are included in the text.

The following workflow starts from a single all-atom structure that is converted into a coarse-grained model system.

1. Construct an all-atom model of the system you want to study, with the periodic boundary conditions specified.

   This all-atom model is essentially a Desmond model system (CMS file), but the force-field parameters are not needed. There are two main options for constructing the all-atom model system.

   • Use the Disordered System Builder Panel to construct a model system from a set of molecules. If you are modeling polymers, you can use the Polymer Builder Panel to build the polymers, then use those to build a disordered system. Specific settings to use when building the disordered system are described in Constructing Disordered Systems for Coarse-Grained Modeling.
   • Use the System Builder Panel to convert a structure into a Desmond model system. This option allows you to convert a wide range of structures into Desmond model systems.

2. Convert the atoms in the all-atom model into coarse-grained particles.

   This step is done in the Map Atoms to Particles Panel. There are many predefined particle types (i.e. molecules or molecular fragments) available in the panel that can be used to map atoms to particles.

   You may want to define your own atom-particle mappings, which you can do for the all-atom system in the Define Groups by SMARTS Panel. When the output from the job is used in the Map Atoms to Particles Panel, the results of the SMARTS matching are listed as particle types.

3. For RH systems, adjust the volume to the desired value.

   See Adjusting the Volume for a Repulsive Harmonic System for instructions.

4. Assign force-field parameters using the Coarse-Grained Force Field Assignment Panel.

   Make sure that the nonbonded potential you use is compatible with the choices you made when building the system.

   The output is a new coarse-grained CMS file or a Project Table entry suitable for use in Desmond simulations.

5. Set up and run the Desmond simulation in the MD Multistage Workflow Panel.

   See Setting Up the Coarse-Grained Simulation for information on how to set up stages and make settings. Note that simulations require GPUs.

An alternative workflow is to construct individual coarse-grained particles and then use them to build the coarse-grained model system. This approach may be more suitable for large systems, as the work of identifying the particles is done on a much smaller system.

1. Construct separate all-atom structures of each component of the full system.

2. As needed, define particle types, using the Define Groups by SMARTS Panel.

3. Convert the structures into coarse-grained particles, using the Map Atoms to Particles Panel.

4. Assemble the coarse-grained particles into the full system with periodic boundary conditions, using the Disordered System Builder Panel

   See Constructing Disordered Systems for Coarse-Grained Modeling for instructions on the settings to use.

5. For RH systems, adjust the volume to the desired value.

   See Adjusting the Volume for a Repulsive Harmonic System for instructions.

6. Assign force-field parameters using the Coarse-Grained Force Field Assignment Panel.

   Make sure that the nonbonded potential you use is compatible with the choices you made when building the system.

7. Set up and run the Desmond simulation in the MD Multistage Workflow Panel.

   See Setting Up the Coarse-Grained Simulation for information on how to set up stages and make settings. Note that simulations require GPUs.