VMD-L Mailing List

From: Mehdi Bakhshi (mehdibakhshi1987_at_gmail.com)
Date: Mon Nov 18 2013 - 15:00:54 CST

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/
>