Setting up NAMD, VMD

[Dirowa]

Ted asked me if there is the possibility for students to make ther 3D modeling on a server with VMD and NAMD ( i think commercial or our server)

But i dont think this is going to work since it is also an GPU intensive task. maybe an alternative is to install VMD and NAMD on our linux desktops and let them work on that?

some background VMD and NAMD are software to 3D model proteins and other chemicals. so an UI is required. I can perhaps imagine that some heavy jobs ( for example modeling a protein in fluides , temp , salt concentration and time can be a job, to send to a server) So far as i can see does a commercial server exists from the developers but not documented nor software available to do so our self

Links https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=NAMD https://www.ks.uiuc.edu/Research/vmd/plugins/namdserver/

@hexylena what is your opinion about this?

[hexylena]

But i dont think this is going to work since it is also an GPU intensive task. maybe an alternative is to install VMD and NAMD on our linux desktops and let them work on that?

which machines are you referring to here? Basically none of our bioinformatics tools use GPUs (except guppy I guess?) so I can't imagine it's a problem if we share GPUs for that as well.

[Dirowa]

I,m referring to no machines at all. it is still an open card. I was thinking, cant we just make VM's for them on surfsara with VMD and NAMD installed?

[hexylena]

ahhh gotcha, sorry for the misunderstanding.

cant we just make VM's for them on surfsara

if we can get VMs with GPUs attached? then yea we can do that.

[Dirowa]

• [x] @bazante1 & @Dirowa testing by surfsara research cloud

[Dirowa]

Tested the NAMD and surfsara on the research cloud. Unless they are going to create a desktop with GPU, will it be a possibility further discussion net thurseday

[Dirowa]

absolved by issue https://github.com/Avans-ATGM/Courses/issues/9