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NedaRahmani edited this page Feb 14, 2025 · 8 revisions

Tutorial 1: Creating a Simple Vesicle

The files needed for the tutorial can be manually downloaded here.

This tutorial will create a vesicle using a simple TS file (sphere). We chose this shape because it is small and can be easily run on your local machines. However, the same method applies to other TS files as well.

Start by selecting the Sphere.tsi file. Open it with a text editor to familiarize yourself with its structure. The .tsi file is an output file from DTS (Dynamically Triangulated Surface). It contains structural data about the simulation, including information on vertices, triangles, and the positions of proteins or other molecules. Specifically, the file includes:

  1. Vertices represent points in space, typically defining the geometry of the simulated system. Each vertex includes its coordinates (x, y, z) and a domain identifier.
  2. Triangles define the connections between vertices, forming the surfaces or mesh elements in the simulation. Each triangle references three vertices.
  3. Inclusions represent proteins or other molecular entities, with information about their position, type, and associated vertex.

The first step in converting (backmapping) a TS file into a coarse-grained (CG) structure is to increase the number of vertices using a pointillism operation, which PLM performs. During this step, the two monolayers are also generated.

The command to run this step is:

TS2CG PLM -TSfile Sphere.tsi -bilayerThickness 3.8  -rescalefactor  4   4   4

This command reads the .tsi file and extends the structure based on the specified rescaling factors (Note: in the previous version, the rescalefactor had only one value). The output consists of two folders:

  1. A folder containing visualization files (pointvisualization_data).
  2. A folder that can be read by the CG Membrane Builder (PCG) script (further details provided in the following)

In the pointvisualization_data folder, you will find GROMACS-compatible structure files (.gro) for both the upper and lower monolayers, along with their respective topology files (.top). Additionally, you will find files compatible with common visualization software like ParaView and VMD. You can use TS2CG PLM -h for available flags.

The second step in creating a vesicle is to place lipids on the generated points using PCG. To do this, you'll need to create a .str file that defines the lipid composition for both monolayers. Using any text editor, create an input.str file and include the following content:

[Lipids List]

Domain 0
POPC  1 1 0.64  
End

This specifies that your system will consist of a single lipid domain containing POPC in both the upper and lower monolayers with the same distribution ratio and an area per lipid (APL) of 0.64 nm² for POPC.

Next, we need a lipid structure file (.LIB). This file defines the lipid connectivity, which is used to position the lipid beads onto the points generated earlier. Although creating this file is straightforward, it can be time-consuming if you are working with many different lipids. Fortunately, we already have a Martini3.LIB file that contains all Martini3 lipids. You can find it in the files folder. Using these two files, you can now execute PCG:

TS2CG PCG -str input.str -Bondlength 0.2 -LLIB ./files/Martini3.LIB -defout system

The outputs will be system.gro (the structure file) and system.top (the topology file). These files contain the final vesicle configuration and are ready for further simulation or analysis.

;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  6256     
; domain 0 
 ;  in the lower monolayer 
     POPC  3876

This concludes the TS2CG part of the tutorial. Simulating the created vesicle would be the canonical next step. A script named run_tut1.sh is available in the tut1 folder. This script will generate a POPC vesicle and run the TS2CG outputs using GROMACS:

To run the outputs from TS2CG, follow these steps:

  1. 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.
  2. Energy Minimization without Solvent: Conduct a standard energy minimization, excluding solvent from the system.
  3. Short Equilibration without Solvent: Run a brief equilibration step without solvent.

tut1 Fig. 1. Initial structure of the created POPC vesicle (left) and the vesicle after a brief vacuum simulation using GROMACS (right). Visualized with VMD.

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