Setting Up the Coarse-Grained Simulation

Coarse-grained simulations should be set up in the MD Multistage Workflow Panel. When a coarse-grained system is loaded into this panel the relaxation protocol is disabled to ensure that stages are defined appropriately for coarse-grained simulations. You can define multiple stages, optionally including one or more stages that are intended to relax the system, in addition to the main production stage. Settings can be made by clicking the Advanced Options button, which opens the Desmond — Advanced Options Dialog Box.

As a general rule, a good relaxation protocol is to use either a short Brownian Dynamics simulation or energy minimization, followed by a short Langevin dynamics stage, perhaps at low temperature, to remove energy regions with high levels of strain.

For LJC systems, the volume should be adjusted using high pressures before the main production simulation. An example relaxation procedure is the following:

  1. A Brownian dynamics stage or a minimization stage.
  2. A short simulation stage (0.2ns) at a low temperature and constant volume.
  3. A short simulation stage (0.2ns) at low temperature and 1 bar.
  4. A simulation stage at a pressure between 100 and 1000 bar for 1-5 ns.
  5. A simulation stage at normal pressure for 1-5 ns.

Langevin dynamics may be appropriate during the early relaxation stages to rapidly dissipate excess energy from local hotspots. Simulations on LJC systems can be carried out with the same thermostats and barostats as for all-atom simulations.

For RH systems it is often a good idea to relax the system before the production simulations. An example relaxation procedure is the following:

  1. A Brownian Dynamics or a minimization stage.
  2. A short Langevin dynamics simulation (0.2ns) at low temperature.
  3. A relatively short (~1ns) Langevin dynamics simulation under the conditions of interest.

Due to the purely repulsive nature of RH potentials, simulations should only be performed in a constant volume ensemble, with a Langevin thermostat to control the temperature.

In the main production stage for molecular dynamics or simulated annealing simulations, you may want to increase the size of the time steps. To do this, click the Advanced Options button and make the changes in the Integration tab. If the time steps are increased it might also be advisable or even necessary to increase the characteristic times (tau) for any barostats or thermostats being used in that stage as well.