Step 1 - Set up the Species
Create the Species
We can import the two species we need from some xyz datafiles supplied in the example data:
Species ⇨ Import ⇨ From XYZ…
Choose the
ipa.xyzfile.
Change the name to
IPAby double clicking theNewSpecies tab
Species ⇨ Add Forcefield Terms…
From the available forcefields choose
OPLS-AA/AlcoholsorUFF(your choice!) and click
Leave all other settings as default and click until finished
Now for the water:
Species ⇨ Import ⇨ From XYZ…
Change the name to
waterby double clicking the
Species ⇨ Import ⇨ From XYZ…
From the available forcefields choose
SPC/Fwand click
Leave all other settings as default and click until finished
Each species needs to have a suitable forcefield applied since Dissolve demands that, at the very least, atom types to be assigned to all atoms.
Create Analysis Sites
How many analysis sites you define will of course depend on what you want to calculate - if, indeed, you are calculating anything at all (beyond using the standard correlation function modules). For the sake of example we’ll calculate some centre-of-mass RDFs here, so you’ll need a centre-of-mass site defined for each of the two species. If you want to define more than that, or add orientation to the centre-of-mass sites, etc., please feel free to do so!
To create a center-of-mass site:
Go to the
Select the molecule in the viewer (drag-click over it)
Right click the selection and click ⇨ to create a new site
Click on the section on the bottom-left of the window
Enable the Weight origin by mass option
Repeat for the water molecule!