| Setting up a job |
| |
| There are a few stages in setting up a job with DRF90. |
| 1. |
|---|
| You need to have a good description of the solute/solvent
molecules as they are in vacuo, i.e. you need a geometry and for each atom a charge. |
| 2. |
|---|
| You need to have for both solute and solvent, the macroscopic density
as well as the molecular mass. If the density is not known, you can use rgc to get a reasonable estimate. |
| 3. |
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| Make a choice for the form of the image box. |
| 4. |
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Use solvents to determine either:
- the size of the image box from a given number of solutes/solvents
- the number of solvents that will fit in an image box of a given size |
| 5. |
|---|
Use rgc to generate a starting
configuration of randomly oriented molecules.
[Hint: increase the size of the box slightly if rgc isn't able to put everything in the
box exactly; this may happen for larger numbers of molecules; the Wall Force will make sure that
during the simulation everything will stay inside the box] |
| 6. |
|---|
| Perform a Molecular Dynamics simulation for ca. 20 ps to equilibrate
the system, using a Wall Force to keep the molecules within the box. |
| 7. |
|---|
| Perform a Molecular Dynamics simulation for ca. 50 ps for the
production run, using a Wall Force to keep the molecules within the box. |
