From: John Stone (
Date: Mon Nov 18 2013 - 12:15:49 CST

  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.

  John Stone

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:
> 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

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