Table of contents
No headersA 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:
- Determine the number of co-solvent molecules necessary, given the box dimensions of your system.
- Generate a coordinate file of a single molecule of your co-solvent (i.e.,
urea.gro
). - Use the
-ci -nmol
options of gmx insert-molecules to add the required number of co-solvent molecules to the box. - Fill the remainder of the box with water (or whatever your other solvent is) using gmx solvate or gmx insert-molecules.
- 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.