insane
INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems
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Repository
INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems
Basic Info
- Host: GitHub
- Owner: Tsjerk
- License: gpl-2.0
- Language: Python
- Default Branch: master
- Size: 4.32 MB
Statistics
- Stars: 64
- Watchers: 6
- Forks: 31
- Open Issues: 21
- Releases: 1
Metadata Files
README.md
Insane - A simple, versatile tool for building coarse-grained simulation systems
Insane (INSert membrANE) is a versatile tool to build coarse-grained simulation systems containing solutes, lipid bilayers, and/or solvents. It is initially aimed at the Martini force field but can be used for other models. It can write PDB or gromacs files.
Using insane, you can build a system containing a transmembrane protein included in a lipid bilayer, with water and ions with the following command line:
bash
insane \
-f cg1a0s.pdb \
-l POPC \
-sol W:90 -sol WF:10 \
-salt 0.8 \
-o system.gro -p topol.top
Installation
Insane can be installed either as a single-file program, or as a python module.
Install insane as a single-file program
Insane depends on python (either version 2 or 3) and on the numpy python library. Make sure you have these two requirements installed:
bash
python -c 'import numpy'
If this command line outputs an error message, you need to instal either python or numpy.
Download the latest version of insane as a single executable.
Run insane: ./insane -h.
Install insane as a python module
Insane is available on pypi and can be installed using pip. To install insane for the current user, run
bash
pip install --user insane
Pip installs the insane in ~/.local/lib/python<version>/site-packages,
where <version> is the version of python. Check that the
directory exists and that it is in your PYTHONPATH. The insane program is
installed in ~/.local/bin, make sure this directory is in your PATH.
To install insane system wide, run
bash
sudo pip install insane
We recommend the use of python virtual environments. Read more about them on the MDAnalysis website.
Quick start
Create a simple lipid bilayer
The following command creates a hydrated POPC bilayer:
bash
insane -l POPC -d 10 -dz 7 -sol W -o bilayer.gro -p topol.top
The -l argument tells insane to include the given lipid. The number of lipids
to include is determined from the area per lipid and the size of the box; the
default area per lipid is 0.6 nm².
With -d and -dz, we specify the dimensions of the box. Here we create
a hexagonal prism box where images are separated by 10 nm in the XY plane, and
7 nm in the Z dimension. The shape of the box can be changed with the -pbc
argument.
The -sol argument tells insane to include some solvent in the box. Here we
include Martini water. The total amount is defined from the free volume of the
box, and the solvent diameter (0.5 nm per default).
The -o and -p arguments specify the output of the program. With -o
bilayer.gro, insane will write the system structure in a GRO
file usable with
gromacs. Insane can also write PDB files if the output file has the '.pdb'
file extension. With -p topol.top, insane will write a template TOP file to
be used with gromacs. If the -p argument is omitted, insane writes the
content of the system on the standard output in a form that can be appended at
the end of an existing TOP file.
Create a more complex bilayer
Insane can build lipid mixtures. Here we build a ternary mixture containing a fully saturated lipid (DPPC), a polyunsaturated lipid (dilinoleyl-phosphatidylcholine, called DIPC in the Martini force field), and cholesterol.
bash
insane \
-o bilayer.gro -p topol.top \
-x 20 -y 20 -z 10 \
-l DPPC:4 -l DIPC:3 -l CHOL:3 \
-sol W:90 -sol WF:10
The periodic box can be defined in multiple ways. Here we build an orthorhombic
box by setting the X, Y, and Z axes separately with -x, -y, and -z,
respectively.
The -l option can be provided multiple times to setup multiple lipid types.
Here we setup DPPC, DIPC, and cholesterol with a 4:3:3 ratio.
The -sol option can also be provided multiple times. Here the solvent is
composed of 90% of regular Martini water and 10% Martini anti-freeze water.
Solvate a protein
Insane can setup protein systems. Here we create a box of solvent around a protein. Note that insane does not prepare the protein itself. Use martinize to coarse grain a protein structure.
bash
insane -o system.gro -p topol.top -f protein.pdb -d 7 -sol W -salt 0
Solutes, including proteins, can be read from a GRO or a PDB file provided with
the -f argument.
With the -d 7 argument, insane builds the periodic box such that the distance
between two periodic images is greater than 7 nm. By default, in the absence of
a membrane, insane builds a rhombic dodecahedral box. Setting the periodic box
with -box, or setting the box geometry with -pbc, overwrite that default.
If the -salt argument is set, insane will add ions to the system. With
-salt set to 0, insane will add enough chloride or sodium ions to
neutralize the system charge. If -salt is set to any positive value, it is
read as the concentration of ions in molar.
Insert a protein in a membrane
Now that we have seen how to build a membrane and how to build a protein system, we can insert a protein in a lipid bilayer.
bash
insane \
-o system.gro -p topol.top \
-d 10 -pbc hexagonal \
-l POPC -sol PW \
-f protein.gro -center
Here, the protein structure we give with the -f argument is centered in the
box along the Z axis with the -center argument.
We build this system with Martini polarizable
water
using -sol PW.
With the -pbc option we set the shape of the periodic box to a prism with
a hexagonal base.
Changing templates
Templates for both Martini 2 and 3 molecules are predefined within insane, use the -ff M2 or -ff M3 to switch between them. Specific template versions can also be specified directly in the lipid name e.g. use -l M3.POPC instead of -l POPC.
Definitions of lipid templates are stored in the insane/lipids.dat file and can be viewed and edited there.
Get help
Get the list of all the arguments by running insane -h.
You can get additional help in the "Tools" section of the Martini forum.
As well as access tutorials using insane in Martini 2 membrane tutorials and Martini 3 membrane tutorials.
Contribute
Insane is hosted on Github. Please, report there any issue you encounter.
Owner
- Login: Tsjerk
- Kind: user
- Repositories: 6
- Profile: https://github.com/Tsjerk
GitHub Events
Total
- Issues event: 4
- Watch event: 19
- Issue comment event: 7
- Pull request review event: 1
- Pull request event: 4
- Fork event: 7
Last Year
- Issues event: 4
- Watch event: 19
- Issue comment event: 7
- Pull request review event: 1
- Pull request event: 4
- Fork event: 7
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Jonathan Barnoud | j****n@b****t | 106 |
| Tsjerk A. Wassenaar | t****w@g****m | 86 |
| helgi | i****n@g****m | 5 |
| ojeda-e | e****e@u****a | 2 |
| Amirali | a****h | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 39
- Total pull requests: 57
- Average time to close issues: 11 months
- Average time to close pull requests: 2 days
- Total issue authors: 25
- Total pull request authors: 9
- Average comments per issue: 1.0
- Average comments per pull request: 0.3
- Merged pull requests: 50
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 5
- Average time to close issues: about 1 month
- Average time to close pull requests: 3 minutes
- Issue authors: 4
- Pull request authors: 3
- Average comments per issue: 0.4
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jbarnoud (9)
- BartBruininks (3)
- biomolsim (2)
- ignasisg (2)
- fgrunewald (2)
- mimischi (2)
- zamydm (1)
- farmacyst99 (1)
- chaofan520 (1)
- georopon (1)
- kong1-731 (1)
- Tsjerk (1)
- ijpulidos (1)
- ishwar84-cloud (1)
- mnmelo (1)
Pull Request Authors
- jbarnoud (47)
- Ingolfsson (2)
- russellb23 (2)
- MDSYN2019 (2)
- ojeda-e (1)
- cailynsak24 (1)
- jvuo (1)
- amiralih (1)
- Tsjerk (1)
Top Labels
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Packages
- Total packages: 1
-
Total downloads:
- pypi 380 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 3
- Total maintainers: 1
pypi.org: insane
A versatile tool for building membranes and/or solvent with proteins.
- Homepage: https://github.com/Tsjerk/Insane
- Documentation: https://insane.readthedocs.io/
- License: GPLv2
-
Latest release: 1.2.0
published over 2 years ago
Rankings
Maintainers (1)
Dependencies
- numpy *
- simopt *