Since people often have issues getting VMD to work in the terminal, I created this video recently: th-cam.com/video/lWPZAHQiTSs/w-d-xo.htmlsi=woZ44UP1dDg6UI2U
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?
can someone please help me, ı am unable to run text mode for vmd. it gives -bash: vmd: command not found. vmd -dispdev text -e ubq.pgn with this code on mac
If you can open VMD with the mouse but not using ther terminal, then it sounds like maybe you don't have a correct alias for the vmd command in your ~/.bash_profile or ~/.bashrc file. I'm not 100% sure this is your issue, but I've seen students have symptoms like this before. VMD used to create the alias for you upon installation, but it doesn't seem to always happen automatically now. Good luck!
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?
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.
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.
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?
@@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..?
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*
Since people often have issues getting VMD to work in the terminal, I created this video recently: th-cam.com/video/lWPZAHQiTSs/w-d-xo.htmlsi=woZ44UP1dDg6UI2U
Thank you Dr. Gianmarc .. Great Tutorial
i can't change the directory in tkconsole even though it works for command prompt/terminal. Please help
I am getting error for TCL namdcph
Kindly help me to solve this problem.
how to apply External electric field ON A Molecule using NAMD/ VMD
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?
can someone please help me, ı am unable to run text mode for vmd. it gives -bash: vmd: command not found. vmd -dispdev text -e ubq.pgn with this code on mac
If you can open VMD with the mouse but not using ther terminal, then it sounds like maybe you don't have a correct alias for the vmd command in your ~/.bash_profile or ~/.bashrc file. I'm not 100% sure this is your issue, but I've seen students have symptoms like this before. VMD used to create the alias for you upon installation, but it doesn't seem to always happen automatically now. Good luck!
Can't thank you enough! You are a hero.
I’m so glad it was helpful, thank you for your message!
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.
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?
Google topotools mergemol VMD, you will get a TCl script. You can use that to merge them.
@@mudgalsdiary thanks
Can ubuntu have access such as discovery studio, molecular docking gold?
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?
What temperature should I choose while designing drug for human? Some say it should be 310k as human body temperature other say 300k.
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.
It should be 310k. It's a human body temperature.
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?
Hello. Which version of NAMD do you have?
Hello, it's NAMD 2.14 for Linux-x86_64-multicore
Thanks for this you really helped me
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.
Thanks for posting.
You are very welcome, thank you for your message!
Thanks a lot, Sir! That was very helpful!
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?
This is a demo where I am running through a tutorial specifically for the NAMD molecular dynamics software package.
@@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..?
thanks!!!
gozuuu
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*