GROMACS modification: Yes/No
For a while now, some interesting questions have been wandering through my mind about the permeation study of small solutes molecules across modeled bilayer. The questions go thus: In a situation whereby two solute molecules are inserted into the bilayer for PMF calculation with umbrella sampling,
- At what maximum and minimum positions along the chosen coordinate(e.g let’s say the the chosen coordinate is bilayer normal, z-coordinate) should the two solutes be separated?
- Could anyone please share with me sample pull codes to generate initial configurations that have been used in the past while studying the permeation of small molecules across model bilayers?
- How do we come up with an efficient pull code for final umbrella sampling runs to be used for such system ?