Mixed Solvents

A common question that new users have is how to create a system with mixed solvent (urea or DMSO at a given concentration in water, for example).  The simplest procedure for accomplishing this task is as follows:

1. Determine the number of co-solvent molecules necessary, given the box dimensions of your system.
2. Generate a coordinate file of a single molecule of your co-solvent (i.e., urea.gro).
3. Use the -ci -nmol options of gmx insert-molecules to add the required number of co-solvent molecules to the box.
4. Fill the remainder of the box with water (or whatever your other solvent is) using gmx solvate or gmx insert-molecules.
5. Edit your topology to #include the appropriate .itp files, as well as make changes to the [ molecules ] directive to account for all the species in your system.