Relaxing a Model System
relaxation protocol
Relaxation of a system is an essential part of an MD simulation, as the system that is freshly built may have a large degree of strain. Only when the system is relaxed is it useful to proceed to a production simulation, where the properties of the system at the given temperature and pressure can be analyzed.
The stages in the default relaxation process for the NPT ensemble are:
|
1.
|
Simulate in the NVT ensemble with Brownian dynamics at 10 K with small time steps and solute non-hydrogen atoms restrained |
|
2.
|
Simulate in the NVT ensemble using a Langevin thermostat with: |
- a simulation time of 12ps
- a temperature of 10K
- a fast temperature relaxation constant
- velocity resampling every 1ps
- non-hydrogen solute atoms restrained
|
3.
|
Simulate in the NPT ensemble using a Langevin thermostat and a Langevin barostat with: |
- a simulation time of 12ps
- a temperature of 10K and a pressure of 1 atm
- a fast temperature relaxation constant
- a slow pressure relaxation constant
- velocity resampling every 1ps
- non-hydrogen solute atoms restrained
|
4.
|
Simulate in the NPT ensemble using a Langevin thermostat and a Langevin barostat with: |
- a simulation time of 12 ps
- a temperature of 300 K and a pressure of 1 atm
- a fast temperature relaxation constant
- a slow pressure relaxation constant
- velocity resampling every 1ps
- non-hydrogen solute atoms restrained
|
5.
|
Simulate in the NPT ensemble using a Langevin thermostat and a Langevin barostat with: |
- a simulation time of 24ps
- a temperature of 300K and a pressure of 1 atm
- a fast temperature relaxation constant
- a normal pressure relaxation constant
This protocol is used for the NPAT and NPγT ensembles as well. A similar protocol is used for the NVT ensemble.
The protocol files can be found in $SCHRODINGER/mmshare-vversion/data/desmond. The procedure follows a similar pattern as for NPT.