VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 18 2013 - 12:15:49 CST

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/