{"id":16510804,"url":"https://github.com/cbouy/dashmd","last_synced_at":"2025-10-28T03:31:57.325Z","repository":{"id":45755210,"uuid":"212560693","full_name":"cbouy/DashMD","owner":"cbouy","description":"Real time monitoring and visualization of Amber MD simulations","archived":false,"fork":false,"pushed_at":"2020-02-06T16:10:41.000Z","size":1433,"stargazers_count":15,"open_issues_count":0,"forks_count":5,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-02-01T11:11:09.172Z","etag":null,"topics":["ambermd","bokeh","compchem","computational-chemistry","molecular-dynamics","molecular-modeling","ngl"],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cbouy.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-10-03T11:14:52.000Z","updated_at":"2023-11-11T18:53:43.000Z","dependencies_parsed_at":"2022-09-13T01:11:03.161Z","dependency_job_id":null,"html_url":"https://github.com/cbouy/DashMD","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbouy%2FDashMD","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbouy%2FDashMD/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbouy%2FDashMD/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cbouy%2FDashMD/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cbouy","download_url":"https://codeload.github.com/cbouy/DashMD/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":238590596,"owners_count":19497350,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["ambermd","bokeh","compchem","computational-chemistry","molecular-dynamics","molecular-modeling","ngl"],"created_at":"2024-10-11T15:57:26.682Z","updated_at":"2025-10-28T03:31:56.732Z","avatar_url":"https://github.com/cbouy.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DashMD\n\nReal time monitoring and visualization of Amber MD simulations\n\nDashMD let's you track the status, temperature, pressure, volume, density, and energy of your currently running simulation in an interactive way.\nYou can also plot the RMSD of your trajectories and visualize them directly with [NGL](https://github.com/arose/ngl).\n\n## Screenshots\n\n#### Main tab\n\u003cimg src=\"https://user-images.githubusercontent.com/27850535/71206876-f3981500-22a5-11ea-9a33-2c394872eb50.png\" width=500\u003e\n\n#### Visualization\n\u003cimg src=\"https://user-images.githubusercontent.com/27850535/71206898-001c6d80-22a6-11ea-8efe-2551cbd4b06d.png\" width=500\u003e\n\n#### RMSD tab\n\u003cimg src=\"https://user-images.githubusercontent.com/27850535/71206907-06aae500-22a6-11ea-8707-35c85c74fc4a.png\" width=500\u003e\n\n#### Density tab\n\u003cimg src=\"https://user-images.githubusercontent.com/27850535/71206923-0c082f80-22a6-11ea-95c8-f2ed11dd53dc.png\" width=500\u003e\n\n## Installation\n\nDashMD runs on python and a bit of JavaScript, and depends on the following python packages: `pandas, bokeh, pytraj` which are all automatically installed as requirements. To install, simply run the following command :\n\n```bash\n  pip install git+https://github.com/cbouy/DashMD.git\n```\n\n## Usage\n\nSimply type `dashmd` in a terminal and it should open a new tab in your web browser.\n\n:warning: Currently, DashMD expects all of your files (mdinfo, prmtop, mdout, mdcrd/netcdf) to be in the same directory.\n\nStart by navigating to the folder containing the `mdinfo` file then press on the `Load` button (which should turn green if the folder contains a `mdinfo` file). The Temperature, Pressure...etc will automatically be read from the mdinfo file and plotted on the corresponding tabs, and the structure from the latest Amber Restart file will be plotted on the `View` tab.\n\nIn order to plot the Temperature, Pressure...etc. for a specific simulation file, select the MDOUT file (bottom of the Dashboard tab, only files ending in `.mdout` or `.out` will be listed), then press `Plot`. This might take a while depending on the size of the file.\n\nTo visualize a structure or plot the RMSD, click on the corresponding tab and select both Topology file and Trajectory file and click on the corresponding button. Only files ending with `.top`, `.prmtop`, `.parm7` or `.parm` will be listed for the topology. The RMSD calculation is performed by slicing your trajectory in around 200 frames if possible, for faster calculations.\n\nFor the `View` tab, only files with the `.rst` or `.rst7` extension are listed.\n\nFor the `RMSD` tab, only files ending with `.nc`, `.netcdf`, or `.ncdf` will be listed.\nYou can select multiple trajectory files to plot by pressing on the `Ctrl` key on your keyboard while selecting the trajectories.\nYou can restrict the atoms selected for RMSD calculation by specifying a mask as specified in the `pytraj` documentation [here](https://amber-md.github.io/pytraj/latest/atom_mask_selection.html). A `protein` keyword has been added for easier selection of all protein residues (it's a substitute for `:ALA,ARG`... and all of their protonated forms)\n\nIf necessary, more detailed options are available in the command line:\n```\nusage: dashmd [-h] [-v] [--port INT] [--update INT] [--default-dir STR]\n              [--log level]\n\nMonitor and visualize MD simulations from Amber in real time\n\noptional arguments:\n  -h, --help         show this help message and exit\n  -v, --version      Show version and exit\n  --port INT         Port number used by the bokeh server (default: 5100)\n  --update INT       Update rate to check and load new data, in seconds (default: 20)\n  --default-dir STR  Default directory (default: .)\n  --log level        Set level of the logger (default: INFO)\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbouy%2Fdashmd","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcbouy%2Fdashmd","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcbouy%2Fdashmd/lists"}