VMD (Visual Molecular Dynamics) up and running in IRIX
#1
VMD (Visual Molecular Dynamics) up and running in IRIX
I just got VMD up and running on my Tezro under IRIX 6.5.30:

You can download it from the following site, but you do have to register in order to download it:  
https://www.ks.uiuc.edu/Development/Down...geName=VMD

[Image: NiIBRQ0.png]
(This post was last modified: 08-05-2021, 09:04 PM by Irinikus.)
Irinikus
Hardware Connoisseur

Trade Count: (0)
Posts: 3,475
Threads: 319
Joined: Dec 2017
Location: South Africa
Website Find Reply
08-05-2021, 08:04 PM
#2
RE: VMD (Visual Molecular Dynamics) up and running in IRIX
Download requires registration.

My SGI Hardware:
Indy SGI Indy (1997), R5000 @ 180MHz , 256MB RAM, GR3-XZ graphics, SCSI2SD v5.1 w/ 16GB µSD card, IRIX 6.5.22
O2  SGI O² (1996), R5000 @ 180MHz , 256MB RAM, 2 x 2.0GB SCSI HDD, IRIX 6.5
Other bits: SGI Indycam, Yamaha CRW2100SX-VK External SCSI CD drive, more software than you can poke a stick at.
CyberMonkey
SGI/IRIX newbie.

Trade Count: (0)
Posts: 46
Threads: 9
Joined: Feb 2019
Location: Down Under
Find Reply
08-06-2021, 07:19 AM
#3
RE: VMD (Visual Molecular Dynamics) up and running in IRIX
(08-06-2021, 07:19 AM)CyberMonkey Wrote:  Download requires registration.

Registration for this is free!

Here's a link to another site from which you can download models of other molecules for VMD: https://www.physics.upenn.edu/~robertjo/vmd/
Irinikus
Hardware Connoisseur

Trade Count: (0)
Posts: 3,475
Threads: 319
Joined: Dec 2017
Location: South Africa
Website Find Reply
08-06-2021, 07:56 AM
#4
RE: VMD (Visual Molecular Dynamics) up and running in IRIX
I just brought the V12 in the Tezro to its knees by loading one of the proteins from an HIV into VMD! (Just note the frame rate!!!)

[Image: VXleSYn.png]

[Image: nzZtllk.png]

[Image: xR0uA1t.png]

Here's an image of the virus itself:

[Image: lEtwDLk.png]

I just ran the same model on the V880Z and it actually beats the Tezro in this field!!!! (I must admit that this result really pleases me, as it shows the XVR-4000 to have had value in this field!!! Smile )

[Image: MkjuBvw.jpg]

[Image: axKpww4.jpg]

[Image: Ttk51sT.jpg]
(This post was last modified: 08-06-2021, 10:11 AM by Irinikus.)
Irinikus
Hardware Connoisseur

Trade Count: (0)
Posts: 3,475
Threads: 319
Joined: Dec 2017
Location: South Africa
Website Find Reply
08-06-2021, 09:24 AM
#5
RE: VMD (Visual Molecular Dynamics) up and running in IRIX
Here's a comparison of the VMD output quality of the Tezro VS the V880Z!

Tezro:

[Image: VY10Wxu.jpg]

V880Z:

[Image: bpY2vFC.jpg]

The V880Z definitely produces a cleaner image!

Here's the link to the protein part of an HIV's capsid that I used in these tests, so that you can run tests on your machines: http://www.ks.uiuc.edu/~bcgoh/rsv-hex.pdb
(This post was last modified: 08-06-2021, 03:37 PM by Irinikus.)
Irinikus
Hardware Connoisseur

Trade Count: (0)
Posts: 3,475
Threads: 319
Joined: Dec 2017
Location: South Africa
Website Find Reply
08-06-2021, 02:45 PM
#6
RE: VMD (Visual Molecular Dynamics) up and running in IRIX
Hi Irinikus, this looks fantastic.
I am following the link to get a copy of the software as I am keen to see how it performs on my O350 with IR4.
sgi-enthusiast
O2

Trade Count: (0)
Posts: 32
Threads: 8
Joined: Jun 2018
Find Reply
10-17-2021, 12:42 AM
#7
RE: VMD (Visual Molecular Dynamics) up and running in IRIX
What version are you running there Irinikus? Did you compile it from source or what binary did you DL?

Project: Temporarily lost at sea
Plan: World domination! Or something...
vishnu
Tezro, Octane2, 2 x Onyx4

Trade Count: (0)
Posts: 1,245
Threads: 41
Joined: Dec 2017
Location: Minneapolis, Minnesota USA
Find Reply
10-17-2021, 10:55 PM
#8
RE: VMD (Visual Molecular Dynamics) up and running in IRIX
I downloaded it from the site which I liked in my first post.

Here’s the link again: https://www.ks.uiuc.edu/Development/Down...geName=VMD
(This post was last modified: 10-18-2021, 02:55 AM by Irinikus.)
Irinikus
Hardware Connoisseur

Trade Count: (0)
Posts: 3,475
Threads: 319
Joined: Dec 2017
Location: South Africa
Website Find Reply
10-18-2021, 02:54 AM


Forum Jump:


Users browsing this thread: 1 Guest(s)