From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri May 04 2018 - 03:17:20 CDT

Wow, those are impressive numbers. There's also a recent 6M atoms 1us virus
simulation that you've probably allready seen.
https://elifesciences.org/articles/32478#s4

Best,
Ajasja

On Fri, 4 May 2018 at 03:48, McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> Wow, thanks for that. I did not see that page, very useful info there.
> This should help me get started. I wonder if NAMD 2.13 will be able to
> handle this even better since one of the new features listed is preliminary
> support for billion-atom systems.
>
>
> *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 7:35:46 PM
> *To:* McGuire, Kelly
> *Cc:* Vermaas, Joshua; vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: CellPack
>
> Hi,
> One of the standard NAMD benchmarks is a small virus (1M atoms) if you
> want to play with an existing structure in NAMD and VMD. The modeling
> that goes into building a virus from scratch usually takes a hard working
> scientist some months of work just to get started since there are so
> many issues to get right when building all of the pieces (and of course
> just simply because there are a lot of pieces). The complete PSF/PDB
> for STMV can be found in the "Example Simulations" part of the NAMD page
> here:
> http://www.ks.uiuc.edu/Research/namd/utilities/
>
> You can load it into VMD and play around with it to get ideas of what
> this all looks like when completed for a tiny satellite virus.
>
> On the same web page you'll see "20STMV" and "210STMV" files, those
> are replicated copies of STMV used to benchmark the computing horsepower
> required for simulations of larger structures, e.g., HIV.
> The HIV-1 virus capsid our colleague previously simulated is roughly
> 64 times the size that STMV is, as a point of reference...
>
> There are variouis tools and information available that can be used
> to help prepare portions of virus simulations. VMD can work with
> non-standard PDBs to get past the limits of the PDB format up to a
> certain size (e.g. STMV is done that way), but for systems as large
> ast HIV, you have to use special file formats that are unique to
> VMD and NAMD, particularly if you to systems beyond about
> 5 or 10 million atoms in size. You would still use the same tools
> to build your structure and prepare the simulation inputs, but the
> task of constructing such big systems is accordingly more work, and
> every step is slower and more error prone for many reasons.
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, May 04, 2018 at 01:11:39AM +0000, McGuire, Kelly wrote:
> > 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
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > [1]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > [2]http://www.ks.uiuc.edu/Research/vmd/
> >
> > References
> >
> > Visible links
> > 1.
> https://na01.safelinks.protection.outlook.com/?url=http:%2F%2Fwww.ks.uiuc.edu%2F~johns%2F&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cc1b2374f70984038a65108d5b15751bc%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636609910964377586&sdata=U0eAvmkbwazOgCCtAP%2BL0jDGYYG%2Bz0dp4rKf8VtyVdA%3D&reserved=0
> > 2.
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2F&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cc1b2374f70984038a65108d5b15751bc%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636609910964377586&sdata=DIBhgkyPyAdTV24GF5ZymLFrDIwfaY895JhmwoqMemM%3D&reserved=0
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>