Created by Adrià Bravo Vidal

Introduction

On this page, we provide the simulation scheme used in the work "Multi-body fluctuation-induced forces between membrane proteins: Insights from mesoscale simulations" by Adrià Bravo Vidal and Weria Pezeshkian (https://doi.org/10.1101/2025.09.12.675822). Note that data appearing in the plots of this work can be found in 10.5281/zenodo.20365837.

The simulation scheme consists on three steps:

1. Generating the desired initial membrane shape configuration and equilibrating it.
2. Randomly placing inclusions on it with desired features and running simulations again.
3. Analyzing simulations. (Under construction)

Generating initial membrane configurations

In this work, we used two different membrane shapes, a membrane patch subject to periodic boundary conditions in the XY directions and a membrane with spherical shape. In order to generate a dynamically triangulated surface (DTS) in any of these shapes and equilibrating them under any desired constraints, we refer you to the following tutorial and user manual.

Adding inclusions and running production simulation

After equilibration of the membrane has been reached under desired constraint, we can now proceed to randomly place inclusions in the surface with chosen features and run the simulations again. This can be achieved by adding the following lines to your input.dts file:

INCLUSION
Define 2 Inclusions
SRotation Type   K    KG  KP  KL  C0    C0P C0L  lambda   lkg   lkn    cn0
0      Pro1      x    y   0   0   z    0   0 0 0 0 0   
GenerateInclusions
Selection_Type Random
TypeID     1         
Density    rho    

In here, x, y and z corresponds to $\kappa + \Delta\kappa, \Delta\kappa_g, c_o$, respectively, which are defined in the referenced manuscript. $\rho$ refers to the surface coverage (e.g. fraction of vertices occupied by inclusions). Now, simulations can be run by taking the last dts{x}.tsi file that you generated in the equilibration run with the bare membrane and using it as an input topology file for your new run.

Analyzing the simulations

Analysis code will be made available soon.