Pull code for umbrella sampling

User discussions
1

GROMACS version:2021
GROMACS modification: Yes/No
Dear Users,

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,

  1. 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?
  2. 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?
  3. How do we come up with an efficient pull code for final umbrella sampling runs to be used for such system ?

Thank you.

Regards,
Ridwan Sulaimon