VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 04 2018 - 11:02:02 CDT

HI,
  The new versions of VMD and NAMD have both seen heavy work to enable them
to simulate systems in the billion-atom range. While they run, it is
currently still hard going because every step of building such a massive
system is slow going. Just making VMD atom selections of typical complexity
on a billion atoms can take a few seconds!! You have to have a machine with
between 512GB and 1TB of RAM to to be able work on something in this size
range. Needless to say we're working on both tools to make modeling
and simulating complexes of that size practical. As Josh already pointed
out, all of this has to be paired with serious computing resources on the
back-end.

Best,
  John

On Fri, May 04, 2018 at 01:41:58AM +0000, McGuire, Kelly 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:
> [1]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.
> [2]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.
> [3]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
> [4]http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> [5]http://www.ks.uiuc.edu/Research/vmd/
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/Research/namd/utilities/
> 2. 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
> 3. 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
> 4. http://www.ks.uiuc.edu/~johns/
> 5. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/