VMD-L Mailing List

From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Thu May 03 2018 - 20:41:58 CDT

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
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--
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/