Tutorial 2
The files needed for the tutorial can be manually downloaded here.
In this Tutorial, we are going to create a vesicle with a 50/50 mixture of POPC and DOPC in both monolayers, execute PLM using Sphere.tsi and PCG with the provided .str file as follows:
[Lipids List]
Domain 0
POPC 0.5 0.5 0.64
DOPC 0.5 0.5 0.67
End
TS2CG PLM -TSfile Sphere.tsi -bilayerThickness 3.8 -rescalefactor 4 4 4
TS2CG PCG -str input.str -Bondlength 0.2 -LLIB ./files/Martini3.LIB -defout system
The PLM tool reads the .tsi file and extends the structure according to the specified rescaling factors. This generates a set of points based on the desired system size and lipid distribution. The PCG tool places lipids on the generated points, producing two output files:
- system.gro: contains the coordinates and structure of the generated lipid system.
- system.top: the topology file, which should have the following format:
;This file was generated by TS2CG membrane builder script i.e., PCG
[ system ]
Expect a large membrane
[ molecules ]
; domain 0
; in the upper monolayer
POPC 3056
DOPC 3056
; domain 0
; in the lower monolayer
POPC 1893
DOPC 1893
You can find a script named run_tut2.sh in the tut2 folder. This script will generate a mixed POPC/DOPC vesicle and run the TS2CG outputs using GROMACS, following the steps below:
- Energy Minimization with Softcore Potential: Perform a short, 50-step energy minimization using the softcore potential, applying restraints to the lipid headgroups and protein backbones. Note that this step is optional and may not be necessary for all systems.
- Energy Minimization without Solvent: Conduct a standard energy minimization, excluding solvent from the system.
- Short Equilibration without Solvent: Run a brief equilibration step without solvent.
Fig. 2. Initial structure of the created mixed POPC/DOPC vesicle (left) and the vesicle after a brief vacuum simulation using GROMACS (right). Visualized with VMD.