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

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

Thank you Dr. Gianmarc .. Great Tutorial

thank you so much

Thanks for this you really helped me

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?

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.

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?

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

Thanks a lot, Sir! That was very helpful!

Thanks for posting.

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

gozuuu

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.

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

thanks!!!

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

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?

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

Hello. Which version of NAMD do you have?

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.

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

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?

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

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*