How can I create a custom solvent model for Desmond simulations?

Solvent models are essentially Maestro files that contain equilibrated solvent molecules in a unit cell at the desired density, with certain properties supplied. A suggested procedure for creating a solvent box is given below.

The first stage is to create a cubic array of solvent molecules in Maestro, which you can do as follows.

1. Start Maestro, or in an existing Maestro session, ensure that you have an empty project.
2. Import the molecule of interest into Maestro, or build it in Maestro and create an entry from it. Ensure that you give the entry a meaningful title.
3. Open the Project Table and select the entry.
4. Duplicate the entry to create 16 entries, by typing CTRL+A CTRL+D four times.
5. Select all entries (CTRL+A) and include them in the Workspace (CTRL+N).
6. Type tile in the Commands text box (command input area) in the main window. The entries are now placed in a grid in the plane of the Workspace, with new coordinates.
7. In the Project Table panel, choose Entry → Merge. A new entry is created with the molecules from the Workspace.
8. Delete the original set of entries by choosing Select → Invert, then Entry → Delete. There should now be only one entry containing all the molecules.
9. Include the new entry in the Workspace, and choose View → Align
10. Select YZ for Align three or more atoms to a plane, then pick the same atom in three of the molecules. You must ensure that the atoms are not in a straight line, e.g. by picking two from the first row and one from the second.
11. Click Align, then Update Coordinates. The plane of the "sheet" of molecules is rotated and the coordinates are now updated.
12. Duplicate this entry with CTRL+A CTRL+D. (Only do one duplication, because tiling of two entries places them side-by-side, but tiling of more than two creates a grid.)
13. Repeat steps 5 — 7. You should now have a single entry with two "sheets" of molecules.
14. Duplicate this entry with CTRL+A CTRL+D, and repeat steps 5 — 7. You should now have a single entry with four "sheets" of molecules that make up a 4×4×4 box.

For smaller solvent molecules, you should probably double the size of the box, to produce a box whose sides are around 30 Å long. To do so, follow the procedure above from step 3 with this entry as the original "molecule", but make 4 entries instead of 16, and only do one duplication after the realignment.

Now that you have a box of molecules, you can use Desmond to create the solvent model box, as follows:

1. Create a model system without solvent, ions, or membrane in the System Builder panel. Use a cubic box, use the Buffer method for the box size, and enter a distance of 1.0.
2. When the system is built, run a Desmond MD simulation in the NPT ensemble to equilibrate it. The simulation time required is usually only 200–400 ps, but you can use the defaults if you want. Make sure that you select Relax model system before simulation. The simulation randomizes the regular array of molecules, and also ensures that the density is correct for the given temperature and pressure.
3. When the simulation results are incorporated, add a property as follows:
   
   
   1. Choose Property → Add.
   2. Name the property "num component".
   3. Ensure that the type is Integer.
   4. Enter "1" in the Initial value text box.
   5. Click Add.
4. Export the resulting solvent entry to a Maestro file. Most of the required properties were automatically added in the Desmond simulation, except for the one that you added manually, which must be edited.
5. Edit the Maestro file, and change "i_user_num_component" to "i_ffio_num_component".

You can now use this Maestro file as a custom solvent file.

Keywords: Desmond, solvent

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