Potentials and Simulation Types for Coarse-Grained Modeling

Two general types of non-bonded interactions are supported for coarse-grained modeling. You can only use one of these types of potentials in a simulation:

• Lennard-Jones potentials in combination with Coulombic potentials (LJC). A variety of Lennard-Jones potentials beyond the usual 12-6 potentials are supported. Electrostatic interactions are calculated using the particle mesh Ewald (PME) method.
• Repulsive harmonic potentials (RH), like those commonly used in Dissipative Particle Dynamics (DPD) simulations. You should use Langevin dynamics with these potentials, as thermostats with temperature control via interparticle interactions are not supported.

Valence bond, angle, and dihedral potentials, equivalent to those in the OPLS force field function, are supported in combination with both types of non-bonded potentials.The potentials are described in more detail in the Coarse-Grained Force Field Assignment Panel topic.

Although the potentials are only applied to the model system at a late stage in the workflow, you must decide at the beginning which kind of potential you want to use. This is because there are choices that must be made when building the model system that are affected by the choice of potential.

Although coarse-grained models are run with Desmond, the input files (.msj and .cfg) needed for coarse-grained simulations are different from those used for all-atom simulations. Thus you should only use files generated for a coarse-grained system when setting up the job in the MD Multistage Workflow Panel.