Example 2: Biphasic Systems
Example 2: Building Biphasic Systems
The original tutorial was to make a heterogeneous biphasic system composed of hydrophobic (cyclohexane) and hydrophilic (water) layers.
Here we are going to use benzene to replace cyclohexane as a demostration of how to use CHARMM-GUI to make a new ligand.
As we covered before, Gromacs simulations require two starting input files:files for a structure:
- Coordinate file: this can be a Protein Data Bank pdb
filefile, or Gromacs - Toplogy file: this can be a Gromacs top file