VMD

VMD is designed for modeling, visualization, and analysis of biomolecular systems such as proteins, nucleic acids, lipid membranes, carbohydrate structures, etc. VMD provides a wide variety of graphical representations for visualizing and coloring molecular structures: molecular surfaces, space-filling CPK spheres and cylinders, licorice bonds, backbone tubes, and ribbons, secondary structure cartoons, and others.

VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a local or remote computer.

While VMD is typically used interactively in a desktop graphical environment, it can also be used to perform non-interactive (batch mode) analytical calculations and visualization tasks run on both workstations (or single cluster nodes) and in parallel on distributed memory clusters and supercomputers using MPI.

VMD, tutorials, and documentation are available at http://www.ks.uiuc.edu/Research/vmd/

See here for a document describing prerequisites and setup steps for all HPC containers.

See here for a document describing the steps to pull NGC containers.

System requirements

Before running the NGC RELION container please ensure your system meets the following requirements.

One of the following container runtimes\n
- nvidia-docker
- Singularity >= 3.1
\n

x86_64

Pascal(sm60), Volta(sm70), or Ampere (sm80) NVIDIA GPU(s)
CUDA driver version >= r450, -or- r418, -or- r440

arm64

Pascal(sm60), Volta(sm70), or Ampere (sm80) NVIDIA GPU(s)
CUDA driver version >= r450

1. Running VMD

There are two options to run the VMD container.

You can run VMD directly from the docker run command.
You can run the VMD container interactively within the container.

1.1 Running VMD from the command line

In this example,

To run the VMD container from the CLI, issue the following command, which runs VMD and makes\nthe current working directory accessible within the container as \"/workspace\":

docker run -ti --gpus all --rm -v $(pwd):/workspace nvcr.io/hpc/vmd:1.9.4a44 vmd\n

Note you could also point the CLI command to launch VMD on a script located in your working directory instead. The script below starts the VMD container and runs the xxx.vmd script from your workspace directory.

docker run -ti --gpus all --rm -v $(pwd):/workspace nvcr.io/hpc/vmd:1.9.4a44 vmd -dispdev openglpbuffer -e /workspace/xxx.vmd\n

1.2 Running VMD Interactively

In this example, we will run VMD interactively and reproduce an H1N1 test scene included within the container. Running interactively is useful when using VMD for visualization and analysis tasks that may involve external scripting of VMD runs, significant file management within complex directory hierarchies, or when running multiple VMD instances run within the same container and OS image.

To run the VMD container interactively, issue the following command which starts the container and also mounts your current directory to /workspace so it is available inside the container. (see the -v options on the command below to set the mapping of your local data directory to the one inside the container).

docker run -ti --gpus all --rm -v $(pwd):/workspace nvcr.io/hpc/vmd:1.9.4a44\n

After the container starts you will be in the / directory and, you can then change to /workspace and run VMD manually

vmd -dispdev openglpbuffer -e xxxx.vmd\n

Running with Singularity 3.X.Y

This image was verified on Singularity version 3.X.Y. To check the currently installed Singularity version, use:

$ singularity --version\n

Before running with singularity, configure NGC container registry authentication credentials via these environment variables:

$ export SINGULARITY_DOCKER_USERNAME='$oauthtoken'\n$ export SINGULARITY_DOCKER_PASSWORD=\n

More information about obtaining and using an NVIDIA NGC Cloud Services API key can be found here.

To build a singularity image run this:

$ singularity build vmd:1.9.4a44.sif nvcr.io/hpc/vmd:1.9.4a44\n

Run VMD with the image:

$ singularity exec --nv -B : vmd:1.9.4a44.sif vmd\n

Upon success, you will see the VMD command-line interface:

Info) VMD for LINUXARM64, version 1.9.4a44 (June 25, 2020)\nInfo) http://www.ks.uiuc.edu/Research/vmd/                         \nInfo) Email questions and bug reports to vmd@ks.uiuc.edu           \nInfo) Please include this reference in published work using VMD:   \nInfo)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual   \nInfo)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.\nInfo) -------------------------------------------------------------\nInfo) Multithreading available, 56 CPUs detected.\nInfo) Free system memory: 249GB (97%)\nInfo) Creating CUDA device pool and initializing hardware...\nInfo) Detected 2 available CUDA accelerators:\nInfo) [0-1] Tesla V100-PCIE-32GB 80 SM_7.0 1.4 GHz, 32GB RAM AE7 ZC\nvmd &gt; \n

or run it in non-interactive mode:

$ singularity exec --nv -B : vmd:1.9.4a44.sif sh -c \"vmd -dispdev openglpbuffer -e /workspace/xxx.vmd\"\n

2 Suggested Reading

","resourceVersions",[270,271,272,273,274],"resourceVersionsTotal",4,"hasMoreVersions","versionMetadata",{"_247":222,"_92":-5,"_44":248,"_249":-5,"_250":251,"_95":252,"_253":-5,"_254":-5,"_255":26,"_256":-5,"_257":26,"_258":-5,"_259":26,"_260":-5,"_261":26,"_262":-5,"_263":26,"_264":-5,"_265":26,"_266":-5,"_267":26,"_268":269},"versionNotFound","isLoggedIn","latestVersionPath","/orgs/hpc/-/containers/vmd/-","version","1.9.4a44-arm64","imageReference","nvcr.io/hpc/vmd:1.9.4a44-arm64","cliDownloadCommand","helmFetchCommand","viewAllVersionsPath","/orgs/hpc/-/containers/vmd/1.9.4a44-arm64/tags","accessCheckResult",{"_246":168},"hasRelatedCollections","context",{"_87":88,"_89":-7},1786130027674,[],[],[238,239,240,241,242,243,244],{"_40":62,"_42":67,"_44":57,"_46":58,"_48":68,"_50":51},{"_40":62,"_42":65,"_44":57,"_46":58,"_48":66,"_50":51},{"_40":62,"_42":63,"_44":57,"_46":58,"_48":245,"_50":51},{"_40":55,"_42":60,"_44":57,"_46":58,"_48":61,"_50":51},{"_40":55,"_42":56,"_44":57,"_46":58,"_48":59,"_50":51},{"_40":52,"_42":53,"_44":45,"_46":47,"_48":54,"_50":51},{"_40":41,"_42":43,"_44":45,"_46":47,"_48":49,"_50":51},141,"allowed","versionId","NOT_SCANNED","releaseType","createdDate",["D",1594341213520],["D",1594341213520],"totalSizeInBytes","totalFileCount","isSigned","malwareScanStatus","isScanned","releaseNotes","hasReleaseNotes","setup","hasSetup","quickStartGuide","hasQuickStartGuide","advanced","hasAdvanced","performance","hasPerformance","policies",[],{"_80":283,"_276":284,"_249":-5,"_255":26,"_257":26,"_268":282,"_259":26},{"_80":281,"_276":281,"_249":-5,"_255":26,"_257":26,"_268":282,"_259":26},{"_80":222,"_276":222,"_249":-5,"_255":26,"_257":26,"_268":280,"_259":26},{"_80":278,"_276":278,"_249":-5,"_255":26,"_257":26,"_268":279,"_259":26},{"_80":275,"_276":275,"_249":-5,"_255":26,"_257":26,"_268":277,"_259":26},"cuda9-ubuntu1604-egl-1.9.4a17","name",[],"1.9.4a44-x86_64",[],[],"1.9.4a44",[],"-","Latest (1.9.4a44)","hpc/vmd","hpc/containers/vmd","vmd","VMD is designed for modeling, visualization, and analysis of biomolecular systems such as proteins, nucleic acids, lipid membranes, carbohydrate structures, etc. VMD provides a wide variety of graphical representations for visualizing and coloring molecular structures: molecular surfaces, space-filling CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, secondary structure cartoons, and others.","# VMD\n\nVMD is designed for modeling, visualization, and analysis of biomolecular systems such as proteins, nucleic acids, lipid membranes, carbohydrate structures, etc. VMD provides a wide variety of graphical representations for visualizing and coloring molecular structures: molecular surfaces, space-filling CPK spheres and cylinders, licorice bonds, backbone tubes, and ribbons, secondary structure cartoons, and others.\n\nVMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a local or remote computer.\n\nWhile VMD is typically used interactively in a desktop graphical environment, it can also be used to perform non-interactive (batch mode) analytical calculations and visualization tasks run on both workstations (or single cluster nodes) and in parallel on distributed memory clusters and supercomputers using MPI.\n\nVMD, tutorials, and documentation are available at [http://www.ks.uiuc.edu/Research/vmd/](http://www.ks.uiuc.edu/Research/vmd/)\n\n[See here](http://docs.nvidia.com/ngc/ngc-user-guide/index.html) for a document describing prerequisites and setup steps for all HPC containers.\n\n[See here](http://docs.nvidia.com/ngc/ngc-user-guide/index.html) for a document describing the steps to pull NGC containers.\n\n# System requirements\nBefore running the NGC RELION container please ensure your system meets the following requirements.\n\n* One of the following container runtimes\n * [nvidia-docker](https://github.com/NVIDIA/nvidia-docker)\n * [Singularity](https://www.sylabs.io/docs/) >= 3.1\n\n## x86_64\n* Pascal(sm60), Volta(sm70), or Ampere (sm80) NVIDIA GPU(s)\n* CUDA driver version >= r450, -or- r418, -or- r440\n\n## arm64\n* Pascal(sm60), Volta(sm70), or Ampere (sm80) NVIDIA GPU(s)\n* CUDA driver version >= r450\n\n\n## 1. Running VMD\n\nThere are two options to run the VMD container.\n\n- You can run VMD directly from the docker run command.\n- You can run the VMD container interactively within the container.\n\n## 1.1 Running VMD from the command line\n\nIn this example,\n\nTo run the VMD container from the CLI, issue the following command, which runs VMD and makes \nthe current working directory accessible within the container as \"/workspace\":\n```bash\ndocker run -ti --gpus all --rm -v $(pwd):/workspace nvcr.io/hpc/vmd:1.9.4a44 vmd\n```\nNote you could also point the CLI command to launch VMD on a script located in your working directory instead. The script below starts the VMD container and runs the xxx.vmd script from your workspace directory.\n```bash\ndocker run -ti --gpus all --rm -v $(pwd):/workspace nvcr.io/hpc/vmd:1.9.4a44 vmd -dispdev openglpbuffer -e /workspace/xxx.vmd\n```\n## 1.2 Running VMD Interactively\n\nIn this example, we will run VMD interactively and reproduce an H1N1 test scene included within the container. Running interactively is useful when using VMD for visualization and analysis tasks that may involve external scripting of VMD runs, significant file management within complex directory hierarchies, or when running multiple VMD instances run within the same container and OS image.\n\nTo run the VMD container interactively, issue the following command which starts the container and also mounts your current directory to /workspace so it is available inside the container. (see the -v options on the command below to set the mapping of your local data directory to the one inside the container).\n```\ndocker run -ti --gpus all --rm -v $(pwd):/workspace nvcr.io/hpc/vmd:1.9.4a44\n```\nAfter the container starts you will be in the / directory and, you can then change to /workspace and run VMD manually\n\n```bash\nvmd -dispdev openglpbuffer -e xxxx.vmd\n```\n\n# Running with Singularity 3.X.Y\n\nThis image was verified on Singularity version 3.X.Y. To check the currently installed Singularity version, use:\n\n```bash\n$ singularity --version\n```\n\nBefore running with `singularity`, configure NGC container registry authentication credentials via these environment variables:\n\n```bash\n$ export SINGULARITY_DOCKER_USERNAME='$oauthtoken'\n$ export SINGULARITY_DOCKER_PASSWORD=\n```\nMore information about obtaining and using an NVIDIA NGC Cloud Services API key can be found [here](http://docs.nvidia.com/ngc/ngc-user-guide/index.html).\n\nTo build a singularity image run this:\n\n```bash\n$ singularity build vmd:1.9.4a44.sif nvcr.io/hpc/vmd:1.9.4a44\n```\n\nRun VMD with the image:\n\n```bash\n$ singularity exec --nv -B : vmd:1.9.4a44.sif vmd\n```\n\nUpon success, you will see the VMD command-line interface:\n\n```bash\nInfo) VMD for LINUXARM64, version 1.9.4a44 (June 25, 2020)\nInfo) http://www.ks.uiuc.edu/Research/vmd/ \nInfo) Email questions and bug reports to vmd@ks.uiuc.edu \nInfo) Please include this reference in published work using VMD: \nInfo) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual \nInfo) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.\nInfo) -------------------------------------------------------------\nInfo) Multithreading available, 56 CPUs detected.\nInfo) Free system memory: 249GB (97%)\nInfo) Creating CUDA device pool and initializing hardware...\nInfo) Detected 2 available CUDA accelerators:\nInfo) [0-1] Tesla V100-PCIE-32GB 80 SM_7.0 1.4 GHz, 32GB RAM AE7 ZC\nvmd > \n```\n\nor run it in non-interactive mode:\n\n```bash\n$ singularity exec --nv -B : vmd:1.9.4a44.sif sh -c \"vmd -dispdev openglpbuffer -e /workspace/xxx.vmd\"\n```\n\n## 2 Suggested Reading\n\n- VMD Tutorial [(online HTML)](http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/) [(PDF)](http://www.ks.uiuc.edu/Training/Tutorials/vmd/vmd-tutorial.pdf) [(Required tutorial files -- Unix tar.gz format)](http://www.ks.uiuc.edu/Training/Tutorials/vmd/vmd-tutorial.pdf)\n- [List of other tutorials for VMD, NAMD, and Lattice Microbes](http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/)\n- [Molecular cell biology case studies taught with interactive VMD molecular graphics](http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/)",["D",1594341354570],"UIUC",[281,222,278,275],"/api/image/hpc/-/containers/vmd",756212512,"hasSignedTag",[],[301,302,303,304,305],[],[],[],{"_93":317,"_128":317,"_129":318,"_131":132},{"_93":313,"_128":314,"_129":315,"_131":132},{"_93":310,"_128":311,"_129":312,"_131":132},{"_93":308,"_128":308,"_129":309,"_131":132},{"_93":306,"_128":306,"_129":307,"_131":132},"X86_64",{"_133":132,"_128":306},"Visualization",{"_133":132,"_128":308},"HPC","pltfm_hpc",{"_133":166,"_128":311},"High Performance Computing","uscs_high_performance_computing",{"_133":316,"_128":314},"application","Arm64",{"_133":132,"_128":317},{"_189":1300,"_191":1301},"ngcApps",[1253],"csaApiBaseUrl","https://www.nvidia.com/ai-agents/csa-agent/dcsm","datadogRum",{"_1234":1235,"_1236":1237,"_1238":1239,"_1240":1241,"_1242":330,"_221":358,"_1243":1244,"_1245":51,"_1246":168,"_1247":168,"_1248":1249,"_1250":168,"_1251":1252},"amplitude",{"_1231":1232,"_872":-7,"_1233":26},"disableJs","environment","prod","featureFlagsBlob","JTdCJTIydGVzdEZsYWclMjIlM0FmYWxzZSUyQyUyMnNob3dTZWFyY2hMYWJlbFNldEZpbHRlcnMlMjIlM0FmYWxzZSUyQyUyMmVuYWJsZUNzYVdpZGdldCUyMiUzQWZhbHNlJTJDJTIyZW5hYmxlUHJvZHVjdEdyb3VwaW5nQnlTdWJzY3JpcHRpb24lMjIlM0FmYWxzZSUyQyUyMmNvbnRhaW5lclNjYW5uaW5nUmVkZXNpZ25NMiUyMiUzQWZhbHNlJTdE","featureFlagsGuarded","isDevLikeEnv","isPlaywright","isMobileDevice","categorizedOrgs",{"_1225":1226,"_1227":1228,"_1229":1230},"currentOrgContext","currentContextRoles",[],"enterpriseOrgs",[],"manageableExternalUserGroups",[],"locale","en","ngcApiOrigin","ngcHelmOrigin","origin","https://catalog.ngc.nvidia.com","usesMocks","theme","year",2026,"now",1786130027533,"1.11.0","defaultSearchSuggestions",{"_1112":440,"_1113":1114,"_1115":1116,"_1117":1118},"announcements",[],"consentState",{"_397":1102,"_1103":26,"_1104":26,"_1105":168,"_1106":1107},"consentConfig",{"_379":380,"_381":382,"_383":384,"_385":386,"_387":388,"_389":390,"_391":392,"_393":394,"_395":396,"_397":398},"showContactAdmin",1786130027534,[],[],[372,373,374,375,376,377,378],{"_40":62,"_42":67,"_44":64,"_46":-5,"_48":-5,"_50":51},{"_40":62,"_42":65,"_44":64,"_46":-5,"_48":-5,"_50":51},{"_40":62,"_42":63,"_44":64,"_46":-5,"_48":-5,"_50":51},{"_40":55,"_42":60,"_44":64,"_46":-5,"_48":-5,"_50":51},{"_40":55,"_42":56,"_44":64,"_46":-5,"_48":-5,"_50":51},{"_40":52,"_42":53,"_44":45,"_46":47,"_48":54,"_50":51},{"_40":41,"_42":43,"_44":64,"_46":-5,"_48":-5,"_50":51},"mainInfoText","We and our third-party partners (including social media, advertising, and analytics partners) use cookies and other tracking technologies to collect, store, monitor, and process certain information about you when you visit our website. 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They are capable of tracking your browser across other sites and building up a profile of your interests. This may impact the content and messages you see on other websites you visit. If you do not allow these cookies you may not be able to use or see these sharing tools.","alwaysActive","order",11,"cookies",[],"hosts",[],"C0004","Advertising Cookies","These cookies record your visit to our websites, the pages you have visited and the links you have followed to influence the advertisements that you see on other websites. These cookies and the information they collect may be managed by other companies, including our advertising partners, and may be used to build a profile of your interests and show you relevant advertising on other sites. We and our advertising partners will use this information to make our websites and the advertising displayed on it, more relevant to your interests.",5,[537,538,539,540,541,542,543,544,545,546,547,548,549,550,551,552,553,554,555,556,557,558],[421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437],{"_438":532,"_93":532,"_92":440,"_411":533},{"_438":528,"_93":528,"_92":440,"_411":529},{"_438":523,"_93":523,"_92":440,"_411":524},{"_438":519,"_93":519,"_92":440,"_411":520},{"_438":514,"_93":514,"_92":440,"_411":515},{"_438":509,"_93":509,"_92":440,"_411":510},{"_438":501,"_93":501,"_92":440,"_411":502},{"_438":493,"_93":493,"_92":440,"_411":494},{"_438":488,"_93":488,"_92":440,"_411":489},{"_438":483,"_93":483,"_92":440,"_411":484},{"_438":478,"_93":478,"_92":440,"_411":479},{"_438":473,"_93":473,"_92":440,"_411":474},{"_438":468,"_93":468,"_92":440,"_411":469},{"_438":461,"_93":461,"_92":440,"_411":462},{"_438":456,"_93":456,"_92":440,"_411":457},{"_438":449,"_93":449,"_92":440,"_411":450},{"_438":439,"_93":439,"_92":440,"_411":441},"hostName","amazon-adsystem.com","",[442,443],{"_276":448,"_445":439,"_446":26,"_92":447},{"_276":444,"_445":439,"_446":26,"_92":447},"ad-privacy","host","isSession","This domain is owned by online retailer Amazon and is used as part of its affiliate marketing programme.","ad-id","doubleclick.net",[451,452],{"_276":455,"_445":449,"_446":26,"_92":454},{"_276":453,"_445":449,"_446":26,"_92":454},"IDE","This domain is owned by Doubleclick (Google). 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It uses the data gathered from most of these services to profile the interests of web users and sell advertising space to organisations based on such interest profiles as well as aligning adverts to the content on the pages where its customer's adverts appear.","linkedin.com",[490],{"_276":491,"_445":488,"_446":26,"_92":492},"bcookie","This domain is owned by LinkedIn, the business networking platform. It typically acts as a third party host where website owners have placed one of its content sharing buttons in their pages, although its content and services can be embedded in other ways. Although such buttons add functionality to the website they are on, cookies are set regardless of whether or not the visitor has an active Linkedin profile, or agreed to their terms and conditions. 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These cookies may store a unique ID so that our system will remember you when you return. Information collected with these cookies is used to measure and find ways to improve website performance.",[712,713,714,715,716,717,718,719,720,721,722,723,724,725,726,727,728,729,730,731,732,733,734,735,736,737,738,739,740],[692,693,694,695],{"_438":707,"_93":707,"_92":440,"_411":708},{"_438":702,"_93":702,"_92":440,"_411":703},{"_438":501,"_93":501,"_92":440,"_411":699},{"_438":614,"_93":614,"_92":440,"_411":696},[697],{"_276":698,"_445":614,"_446":168,"_92":618},"_gh_sess",[700],{"_276":701,"_445":501,"_446":168,"_92":508},"YSC","bizible.com",[704],{"_276":705,"_445":702,"_446":26,"_92":706},"_BUID","Bizible is a marketing attribution software that tracks the performance of marketing efforts and connects them to revenue, primarily used for B2B environments.","a.usbrowserspeed.com",[709],{"_276":710,"_445":707,"_446":26,"_92":711},"tuid","This domain is owned by Ookla which provides internet speed testing services through its Speedtest application.",{"_276":782,"_445":560,"_446":26,"_92":783},{"_276":767,"_445":781,"_446":168,"_92":768},{"_276":750,"_445":563,"_446":26,"_92":675},{"_276":750,"_445":663,"_446":26,"_92":675},{"_276":779,"_445":560,"_446":26,"_92":780},{"_276":767,"_445":566,"_446":168,"_92":768},{"_276":777,"_445":560,"_446":26,"_92":778},{"_276":767,"_445":563,"_446":168,"_92":768},{"_276":775,"_445":662,"_446":26,"_92":776},{"_276":767,"_445":684,"_446":168,"_92":768},{"_276":747,"_445":563,"_446":26,"_92":749},{"_276":773,"_445":560,"_446":168,"_92":774},{"_276":771,"_445":560,"_446":26,"_92":772},{"_276":769,"_445":560,"_446":168,"_92":770},{"_276":767,"_445":658,"_446":168,"_92":768},{"_276":765,"_445":560,"_446":26,"_92":766},{"_276":763,"_445":560,"_446":26,"_92":764},{"_276":761,"_445":560,"_446":168,"_92":762},{"_276":759,"_445":667,"_446":26,"_92":760},{"_276":747,"_445":658,"_446":26,"_92":749},{"_276":757,"_445":560,"_446":26,"_92":758},{"_276":755,"_445":560,"_446":168,"_92":756},{"_276":753,"_445":560,"_446":26,"_92":754},{"_276":751,"_445":560,"_446":26,"_92":752},{"_276":750,"_445":560,"_446":26,"_92":675},{"_276":747,"_445":748,"_446":26,"_92":749},{"_276":745,"_445":560,"_446":26,"_92":746},{"_276":743,"_445":560,"_446":168,"_92":744},{"_276":741,"_445":560,"_446":26,"_92":742},"_ga_xxxxxxxxxx","Used by Google Analytics to identify and track an individual session with your device.","s_ppvl","This cookie is set by Adobe Analytics to store information on the percentage of the page displayed to the end user.","coveo_visitorId","This cookie name is associated with Coveo which is used to store a unique user ID for marketing purposes and to track the number of distinct users who submitted a query or clicked an item, counting them only once even if they did the same query or clicked the same item over the course of many visits.","_dd_s","marketplace.nvidia.com","Datadog Cookie used to group all events generated from a unique user session across multiple pages. 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