Hi guys, Welcome to the Advanced Video Search Engine, and you are watching Intro to Running Molecular Dynamics Simulations with NAMD (links to each section in description). That video is uploaded by Gianmarc Grazioli at 2021-01-22T14:33:24-08:00. We are promoting this video only for entertainment and educational purpose only. So, I hope you like & enjoy it. [xS4r2bLATvo]
| Name | Intro to Running Molecular Dynamics Simulations with NAMD (links to each section in description) |
| Video Uploader | Video From Gianmarc Grazioli |
| Upload Date | This Video Uploaded At 22-01-2021 22:33:24 |
| Video Discription | 1:20 - (1) The NAMD tutorial files 4:17 - (2) Running Ubuntu on VirtualBox (included because my Mac is running Catalina, which breaks standard VMD distributions) 6:23 - (3) Preparing simulation files for NAMD using VMD 15:34 - (4) Viewing Molecules in VMD 16:53 - (5) Using Tk Console to generate a PDB file 23:15 - (6) Using VMD script to create a psf file 36:26 - (7) Solvating the protein in a water sphere 45:07 - (8) Visually inspecting the solvated protein using VMD 50:15 - (9) Using .conf script files to control NAMD 1:03:19 - (10) Transferring files to the high performance computing cluster 1:13:18 - (11) Editing files on the computing cluster servers with vi 1:19:30 - (12) Running the NAMD simulation on the hpc server 1:40:34 - (13) Visualizing the NAMD simulation data with VMD Helpful links: 1) Get NAMD - https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD 2) Get VMD - https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD 3) NAMD tutorial with supporting files - http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html 4) Requesting an interactive node with Slurm - https://hpc-uit.readthedocs.io/en/latest/jobs/interactive.html 5) Great video on using vim - https://youtu.be/ggSyF1SVFr4 6) Place to download Charmm forcefields (not needed in video, but good to have handy) - http://mackerell.umaryland.edu/charmm_ff.shtml Grazioli Research Group website - http://gianmarc.com/ xS4r2bLATvo |
| Category | Science & Technology |
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