labioquim / visualdynamics

Web Platform made with Python and NextJS for automating GROMACS simulations

Visual Dynamics

Visual Dynamics is a web application made platform for molecular simulations. It aims to automatize the generation and execution of a molecular simulation with capabilities to generate and run dynamics of Protein and Protein + Ligand (prepared in ACPYPE or PRODRG).

Self-hosting

If you want to self-host Visual Dynamics just stick to the steps below (this only works on Linux):

1. Make sure to have nodejs, yarn, docker , docker compose and the docker plugin nfsvol.
2. Copy the file .env.example to .env and fill it. The ones you need to change are: VISUALDYNAMICS_URL (for this tutorial we'll assume this is set to visualdynamics.localhost), DB_USER, DB_PASS and DB_DATABASE, NEXTAUTH_SECRET, SMTP_USER, SMTP_HOST, SMTP_PASS and SMTP_PORT
3. Run docker compose -f docker-compose.prod.yml up -d --build
4. Enter the folder client and run yarn install.
5. Run DATABASE_URL=postgres://DB_USER:DB_PASS@localhost:5432/DB_DATABASE yarn prisma migrate deploy. Note the DB_ fields that must be the ones you set on .env
6. Run DATABASE_URL=postgres://DB_USER:DB_PASS@localhost:5432/DB_DATABASE yarn prisma db seed. Note the DB_ fields that must be the ones you set on .env
7. Now you can open a browser and access visualdynamics.localhost.

Note: This tutorial will make Visual Dynamics available on only ONE machine.

Note: If you plan to run Visual Dynamics to your whole institution, please coordinate with your IT Sector to address the intricacies of your institution infrastructure.

License

The Visual Dynamics source code is available under the MIT License. Some of the dependencies are licensed differently, so watch out for them.