September 2022

This dataset contains most trajectories used for preparation of following manuscript: 
"Scaling protein-water interactions in the Martini 3 coarse-grained force field to simulate transmembrane helix dimers in different lipid environments"
By the authors: Ainara Claveras Cabezudo, Christina Athanasiou, Alexandros Tsengenes and Rebecca C. Wade. 

The data in this repository is organised in three folders: 

1. no_protein_M3: contains simulations of DPC micelle assembly with Martini 3 in absence of any transmembrane protein. Different DPC concentrations were used:
  
  - 100 DPC molecules
  - 120 DPC molecules
  - 140 DPC molecules 
  - 160 DPC molecules
  - 180 DPC molecules
  - 200 DPC molecules

2. no_protein_M2: contains simulations of DPC micelle assembly with Martini 2 in absence of proteins. Simulations were only run with 100 DPC molecules.  
 


3. GpA: contains simulations with a GpA transmembrane dimer either in a POPC bilayer or a DPC micelle environment. For each case, simulations with and without scaling of protein-water non-bonded interactions are provided. In a subset of simulations, equilibration was run with a scaling factor, which was released in the production runs. These are contained in respective subfolders named "removing_scale_factor". 

4. TrkA: contains simulations with a TrkA transmembrane dimer in a DPC micelle environment. Most simulations were run as tests to provide a solution to the lack of interactions between the hydrophobic tails of DPC and the protein. Some of this tests base on an up-scaling of protein-lipid interactions, while the rest focus on alternative choices of DPC parameters. This second group includes simulations in which a smaller size is used for beads forming DPC tails or in which self-interactions between these beads are reduced. 


Note that several replicas are provided for all trajectories in folders 1, 2 and 3. Due to limited memory resources and because the simulations in folder 4. are examples of failed strategies to solve the problems discussed in the manuscript, only one replica is provided for each system. More replicas can be obtained directly from the authors of the manuscript upon request. 

For each trajectory (in .xtc format), a GROMACS structure file (.gro) with the same name is provided.