VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 22 2013 - 23:26:12 CST

Hi,
  If you're running the 64-bit Linux version of VMD, then
I would not expect a segfault unless you ran your machine out of
memory, or found some kind of bug in VMD 1.9.1. Have you tried
running one of the more recent test versions of VMD 1.9.2 yet?:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 18, 2013 at 04:00:54PM -0500, Mehdi Bakhshi wrote:
> Thanks John for replying.
> I am actually running Vmd 1.9.1 on Linux, 64bit.
> Is there a way to increase this memory limit or run vmd in parallel?
> Mehdi
>
> On Mon, Nov 18, 2013 at 1:15 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> What kind of machine are you running on, and which version of VMD?
> It sounds to me like you might be running a 32-bit VMD which would
> hit the per-process memory use limit at about 2GB.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
> On Sun, Nov 17, 2013 at 12:37:46AM -0500, Mehdi Bakhshi wrote:
> > Hi,
> > I'm trying to make a hexagonal prism of Si3N4 using inorganic
> builder in
> > vmd following the same steps described here:
> >
> http://bionano.physics.illinois.edu/Tutorials/nanopore-protocols.pdf
> > I want to make a similar nanopore to what these guys do, however
> > everything is bigger, my prism length is 50 nm (instead of 10 nm
> for them)
> > and has a diameter of 25 nm (instead of 9nm for them). I can build
> the
> > structure successfully with more than 2million atoms with no
> errors, but
> > when I try to add bonds using "inorganicBuilder::buildSpecificBonds
> $box
> > {{SI N 1.9}} {true true false} top"
> > i get a "segmentation fault" error. is this because vmd can't
> handle this
> > big system or is it because I run out of memory on my machine?
> >
> > Any ideas are appreciated.
> >
> > thanks,
> > Mehdi
>
> --
> 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/ 

-- 
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/