Simulation of Liposomes in GROMACS

User discussions
1

GROMACS version: 2020.1-1
GROMACS modification: No
Hello,
I recently have begun working with GROMACS in my lab with the purpose of trying to create a simulation of DPPC phospholipid liposome fusion and separation. In essence, we wish to use GROMACS simulation to test the effects of different factors on the rate of fusion and separation, specifically pH and liposome size ratios. I am not sure how to go about this as many of the tutorials I have found on GROMACS seem to focused on protein modelling. I attempted to use “gmx insert-molecules” to create an environment with the phospholipds and water, however the simulation would not run due to a lack of a protein. I am sure I am missing something important in the configuration of the simulation as I have read multiple scientific papers that have used GROMACS to simulate phospholipid bilayers and liposomes. If anyone has any ideas on how I could use GROMACS for this kind of simulation, I would greatly appreciate it.
Thank you

2

A lot of the details involved in setting up simulation systems have to do with which force field you would use to describe the molecules involved (in your case, lipid and water).

I don’t think you need to provide a protein if the system doesn’t have one, but rather use the tutorials as starting point and check the doc of the tools involved.

Regarding any published work, the procedure should typically be described in sufficient detail to be reproducible by scientists with typical skills for this field. It is always possible (especially in papers from recent years) that a paper passed review without fulfilling this requirement. Emailing the corresponding author(s) would be appropriate then (in the same email, please, if more than one).

Giacomo

3

Two straighway means to construct liposomes/vesicles:

  1. CHARMM-GUI
  2. Packmol

The websites for both have sufficient info to start building a liposome.

As Giacomo pointed, papers do give sufficient detail to model the systems. DPPC is a common lipid and FF parameters for this lipid could be easily found for multiple FF.