https://github.com/labioquim/visualdynamics

Web Platform made with Python and NextJS for automating GROMACS simulations
https://github.com/labioquim/visualdynamics

grace gromacs md molecular-dynamics molecular-dynamics-automation molecular-dynamics-simulation

Last synced: about 1 month ago
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Web Platform made with Python and NextJS for automating GROMACS simulations

• Host: GitHub
• URL: https://github.com/labioquim/visualdynamics
• Owner: LABIOQUIM
• License: mit
• Created: 2019-12-06T19:22:45.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2024-05-27T19:32:35.000Z (6 months ago)
• Last Synced: 2024-10-12T16:42:18.508Z (about 1 month ago)
• Topics: grace, gromacs, md, molecular-dynamics, molecular-dynamics-automation, molecular-dynamics-simulation
• Language: TypeScript
• Homepage: https://visualdynamics.fiocruz.br
• Size: 155 MB
• Stars: 28
• Watchers: 2
• Forks: 4
• Open Issues: 10
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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README

        
# Visual Dynamics

[![GitHub](https://img.shields.io/github/license/LABIOQUIM/visualdynamics)](https://github.com/LABIOQUIM/visualdynamics/blob/main/LICENSE)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7585469.svg)](https://doi.org/10.5281/zenodo.7585469)

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](https://nodejs.org/en), [yarn](https://yarnpkg.com/), [docker](https://www.docker.com/) , [docker compose](https://docs.docker.com/compose/install/linux/#install-the-plugin-manually) and the docker plugin [nfsvol](https://github.com/cirocosta/nfsvol).

1. 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`

1. Run `docker compose -f docker-compose.prod.yml up -d --build`

1. Enter the folder `client` and run `yarn install`.

1. 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`

1. 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`

1. Now you can open a browser and access [`visualdynamics.localhost`](http://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](./LICENSE). Some of the dependencies are licensed differently, so watch out for them.