From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu May 03 2018 - 20:11:39 CDT

I see. I'm struggling to find any good papers/tutorials on creating large models like a virus. CellPack has tutorials, but I couldn't seem to get a single PDB for that large of a structure. In theory though, if I did get a PDB, it could be opened in VMD (Linux 64-bit version) and a PSF generated from that PDB? And, from there a short simulation set-up if the computing power is available?

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
Sent: Thursday, May 3, 2018 6:57:08 PM
To: johns_at_ks.uiuc.edu; McGuire, Kelly
Cc: vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: CellPack

Yes. With some pretty major caveats of things breaking from time to time when you come across a limitation nobody had come across yet. CellPack doesn't by itself buy you the psf you'd need to run NAMD, but the structures are close enough that a dedicated effort can set up crazy large simulations. Without something like an INCITE allocation though, you may as well forget about it, since the computing requirements are crazy too.

-Josh

On 2018-05-03 18:38:16-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

Out of curiosity, is NAMD capable of simulating something as large as a virus or a complete cell? Where do I begin learning on how to assemble a system like that and simulate it?

Kelly L. McGuire

PhD Scholar

Department of Physiology and Developmental Biology

Brigham Young University

LSB 3050

Provo, UT 84602

________________________________
From: John Stone <johns_at_ks.uiuc.edu>
Sent: Thursday, May 3, 2018 9:22:22 AM
To: McGuire, Kelly
Cc: VMD Mailing LIst
Subject: Re: vmd-l: CellPack
Hi,
  This is something we're definitely interested in doing, but
haven't had any free time to work on thus far. If someone is
interested in getting started on this I would be happy to help
them get the ball rolling. At the most basic level, I think that
this could largely be done via scripting. A more sophisticated
implementation might eventually involve some custom molfile plugin code.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 03, 2018 at 04:03:31AM +0000, McGuire, Kelly wrote:
> Are there any plans to integrate CellPack with VMD?
>
> Kelly L. McGuire
>
> PhD Scholar
>
> Department of Physiology and Developmental Biology
>
> Brigham Young University
>
> LSB 3050
>
> Provo, UT 84602

--
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Beckman Institute for Advanced Science and Technology
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http://www.ks.uiuc.edu/Research/vmd/09910964377586&sdata=DIBhgkyPyAdTV24GF5ZymLFrDIwfaY895JhmwoqMemM%3D&reserved=0>