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OpenAWSEM and Open3SPN2 are open-source, cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical accuracy and intrinsic efficiency of the original models, while adding GPU acceleration and the ability to easily modify the forcefield using OpenMM's Custom Forces software framework. By utilizing GPUs, OpenAWSEM and Open3SPN2 achieve a significant speedup in protein and protein-DNA simulations, making them suitable for simulating large proteins and protein-DNA systems. These codes provide a useful tool for the molecular biophysics community, facilitating the study of protein folding, protein-DNA binding, and other cellular processes.
Installation
OpenAWSEM installation
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- To add a location to your PATH environment variable in Linux, you need to do the following:
Open a terminal and run the following command to open the .bashrc file in a text editor:
nano ~/.bashrc - Scroll to the bottom of the .bashrc file and add the following line, replacing /your/path with the location you want to add to the PATH variable:
export PATH=$PATH:/your/path
Note: You can add any environment variable in a similar way:
export VAR=/Some/path/
*Don't add spaces next to the "=" sign - Press CTRL + X to exit the editor, then press Y to save the changes and Enter to confirm the file name.
- Run the following command to apply the changes to the current terminal session:
source ~/.bashrc - Verify that the location was added to the PATH variable correctly by running the following command:
echo $PATH - You should see the new location in the list of paths that is printed to the screen. Keep in mind that you will need to open a new terminal or log out and log back in for the changes to take effect.
Running simulations
Protein simulations
To simulate a small protein using openAWSEM, follow these steps:
- Activate the openmm environment by running the following command in your terminal:
source activate openmm - Set up a simulation folder for your protein by running the following command:
python YOUR_OPENAWSEM_LOCATION/mm_create_project.py 1r69 --frag
If you already have the PDB file for your protein, use the following command instead:
python YOUR_OPENAWSEM_LOCATION/mm_create_project.py PATH_TO_YOUR_PDB/1r69.pdb --frag - Run the simulation using the following command:
python mm_run.py 1r69 --platform CPU --steps 1e5 --tempStart 800 --tempEnd 200 -f forces_setup.py - To compute the energy and Q of your protein, run the following command:
python mm_analysis.py 1r69 > energy.dat
The qvalue can be found in the second column of energy.dat
Note: The forces_setup.py file controls which force (energy) terms will be included in the simulation.
Note 2: If you don't have a GPU available, you may want to consider using http://awsem-md.org. For small proteins, the LAMMPS version could be faster than openAWSEM.
Note 3: Due to size limitations, the data for the paper "OpenAWSEM with Open3SPN2: a fast, flexible, and accessible framework for large-scale coarse-grained biomolecular simulations" is stored in https://app.globus.org/file-manager?origin_id=b4cef8ce-7773-4016-8513-829f388f7986&origin_path=%2FopenAWSEM_data%2F.
DNA simulations
Protein-DNA simulations