Welcome to spica-tools’ documentation!¶
Spica-tools is a suite of programs that support the setup and parameterization of
coarse-grained (CG) molecular dynamics (MD) simulations using SPICA force field
(Surface Property fItting Coarse grAined model, see SPICA-web for details).
The tools can be used with the cg_spica command integrated python codes.
Spica-tools github repository is found at
spica-tools.
Installation¶
The command to invoke the tools in the src/ directory is cg_spica and requires the Python 3 environment. You will need a bash environment to execute the tools using the command in a console. You can download this repository, including the setup file to use the command, with the following command:
git clone git@github.com:SPICA-group/spica-tools.git
Then, change the current directory to the top directory of the repository:
cd spica-tools/
There is a bash script set.sh, to add the path to use the command, run it with the following command:
source set.sh
The path to cg_spica has been added to the PATH environmental variable. Adding the above line to a configuration file such as files .bash_profile may be useful if you need to use the spica-tools frequently. To verify that the commands to integrate python codes in the src/ directory is available in the console, run the following commands:
cg_spica -h
cg_spica map2cg -h
You can see the available options for the commands, if the command path has been correctly added to the PATH. Cg_spica requires several python libraries to execute some codes, including arithmetic operations, and to read trajectory files obtained from MD simulations. These libraries are listed in requirements.txt in the top directory and can be installed using pip with the following command:
pip install -r requirements.txt