Article ID: 1006 - Last Modified: November 19, 2013
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.
Note: Only pure solvents are supported. Solvents that are mixtures (binary solvents) are not supported.
Note: This is a complex procedure. You should follow the steps exactly. If something goes wrong, start again and make sure you have followed every step.
The first stage is to create a cubic array of solvent molecules in Maestro, which you can do as follows. If you have the Materials Science Suite from 2013-3 or later, you can use the Disordered System Builder panel to create the cubic array. You must choose only one component if you use this panel.
- Start Maestro, or in an existing Maestro session, ensure that you have an empty project.
- 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.
- Open the Project Table and select the entry.
- Duplicate the entry to create 16 entries, by typing CTRL+A CTRL+D four times.
- Select all entries (CTRL+A) and include them in the Workspace (CTRL+N).
tilein 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. (Do not use the Tile toolbar button, as this button does not change the coordinates, only the display.)
- In the Project Table panel, choose Entry → Merge. A new entry is created with the molecules from the Workspace. Make sure that it is the only selected entry.
- Delete the original set of entries by choosing Select → Invert, then Entry → Delete. There should now be only one entry containing all the molecules.
- Include the new entry in the Workspace, and choose View → Align
- 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. Do not pick the same atom in three molecules in the same row. Instead, pick two from the first row and one from the second.
- Click Align, then Update Coordinates. The plane of the "sheet" of molecules is rotated and the coordinates are now updated.
- Duplicate this entry once 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.
- Repeat steps 5 – 7. You should now have a single entry with two "sheets" of molecules.
- Duplicate this entry once 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. (If you don't, delete what you have and start over.)
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 4 with this entry as the original "molecule". In step 4, duplicate the molecule by typing CTRL+A CTRL+D two times to make 4 entries instead of 16, and stop after doing step 13 – do not do step 14.
Now that you have a box of molecules, you can use Desmond to create the solvent model box, as follows:
- 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. If you used the Disordered System Builder, skip this step, as the model system is already created.
- Edit the .cms file for the model system and change solute to solvent. There should be only one or two occurrences of this word.
- Open the Desmond Molecular Dynamics panel.
- In the Model system section, choose Import from file from the option menu, and import the edited .cms file.
- Ensure that the Ensemble class is set to NPT.
- Ensure that Relax model system before simulation is selected, otherwise the simulation is likely to fail.
- Set the simulation time. A time of 200–400 ps is usually sufficient, but you can use the defaults if you want.
- Start the simulation. The simulation randomizes the regular array of molecules, and also ensures that the density is correct for the given temperature and pressure.
- When the simulation results are incorporated, add a property as follows:
- Choose Property → Add.
- Name the property "num component".
- Ensure that the type is Integer.
- Enter "1" in the Initial value text box.
- Click Add.
- From Suite 2013-1 on you can edit the internal name in Maestro, as follows:
- Choose Property → Columns → Edit Name/Type.
- Select the property "num component".
- Select Edit internal data.
- From the Family option menu, choose other, and enter "ffio" in the text box.
- Click Save Changes.
- Export the resulting solvent entry to a Maestro file. The required properties were automatically added in the Desmond simulation, except for the one that you added manually.
- If you did not already change the internal name in step 10, 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.
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