Intro to Running Molecular Dynamics Simulations with NAMD (links to each section in description)

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 - www.ks.uiuc.ed...
2) Get VMD - www.ks.uiuc.ed...
3) NAMD tutorial with supporting files - www.ks.uiuc.edu...
4) Requesting an interactive node with Slurm - hpc-uit.readth...
5) Great video on using vim - • Vim Basics in 8 Minutes
6) Place to download Charmm forcefields (not needed in video, but good to have handy) - mackerell.umary...
Grazioli Research Group website - gianmarc.com/

[@setyantotriwahyudi4322]

Thank you Dr. Gianmarc .. Great Tutorial

[@krishnakumarpatel4079]

Can't thank you enough! You are a hero.

[@GianmarcGrazioliPhD]

I’m so glad it was helpful, thank you for your message!

[@ikponwmosaobaseki3645]

Thanks for this you really helped me

[@abhiban66]

Thanks for posting.

[@GianmarcGrazioliPhD]

You are very welcome, thank you for your message!

[@joaoluismossri7526]

Thanks a lot, Sir! That was very helpful!

[@castilloh.gianmarco1048]

gozuuu

[@bettygao2704]

thanks!!!

[@oktavialisti172]

Hi sir, thank you for the video. I saw on the namd input script, you wrote run 2500, what is unit for that sir? does it show a step or what? for example, the step will be moved every 2 ps. meaning that the total simulations time is 2500 x 2 ps= 5000 ps?

[@Neuronworld]

how to apply External electric field ON A Molecule using NAMD/ VMD

[@manjari3112]

hello sir, thanku your tutorial helped me in simulating my protein with ligand. Is it possible to simulate one protein with multiple ligands using NAMD? Please reply.

[@nickjojo4623]

i can't change the directory in tkconsole even though it works for command prompt/terminal. Please help

[@dianaa.valencia3910]

Hello. If I want to make a long simulation (100 ns) for publishing and also a docking, is this procedure appropriate? Or more steps are required? Thanks.

[@RAHULSINGH-bk3nf]

I am getting error for TCL namdcph
Kindly help me to solve this problem.

[@farhadzrarahmed1819]

Hello Sir. your video is really helpful, thanks. l am a new user MD simulation using LAMMPS packages. If you know about running a system using LAMMPS instead of NAMD and could be described it in a short video. I would be very appreciated it.

[@anushkamahajan8186]

Hi Sir,
If I'm heating my system periodically from 0K to 300K, do I need to use Langevin Dynamics?
What would happen if we don't use Langevin dynamics in NAMD config file?

[@zainabahsan2369]

Showing this problem during MD_Run.namd Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_water_ions.str LINE=*set nat ?NATC* FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE ./toppar_water_ions.str LINE=*set nat ?NATC*

[@1998neet]

Can ubuntu have access such as discovery studio, molecular docking gold?

[@maralafshinpour5539]

Hi , Is there any tutorial for NAMD qm/mm?

[@paulocarvalho5688]

Thanks for the video. Could you make a video teaching how to enable the GPUs? Additionally, could you do a simulation with one GPU and then with more than one GPU? Will simulation with more than one GPU be faster than with just 1? If the result is the same, how do you configure NAMD to use all GPUs?

[@shovansarker5403]

What temperature should I choose while designing drug for human? Some say it should be 310k as human body temperature other say 300k.

[@dianaa.valencia3910]

I've seen 310 K in many works, so I think it'll depend on your system. But I guess all the simulations try to be closest to real as possible.

[@ALEJO29905]

It should be 310k. It's a human body temperature.

[@dianaa.valencia3910]

Hello. Which version of NAMD do you have?

[@GianmarcGrazioliPhD]

Hello, it's NAMD 2.14 for Linux-x86_64-multicore

[@ikponwmosaobaseki3645]

what if u have multiple protein chains, will you run psfgen for each chain? if u do that you will have different pdb files how can u merge that?

[@mudgalsdiary]

Google topotools mergemol VMD, you will get a TCl script. You can use that to merge them.

[@ikponwmosaobaseki3645]

@@mudgalsdiary thanks

[@meitadea3765]

hello sir, is this the overall design of molecular dynamics?

[@GianmarcGrazioliPhD]

This is a demo where I am running through a tutorial specifically for the NAMD molecular dynamics software package.

[@godwinir712]

@@GianmarcGrazioliPhD Respected sir..I couldnt acess into the Charmm Gui web server from my personal mail and I am not provided with affiliation mail..could you please help me out..?Or is there another way to generate files..?