From: gurunath katagi (
Date: Mon Jan 26 2009 - 03:10:56 CST

this is tha question regarding the script fo obtain the Calpha-Calpha
distanceof a selection which is available in vmd script library.
My question is : After you obatin the distance map after running the script
.. how do you extract the data from distance map?

thank you..

On Mon, Nov 24, 2008 at 10:30 PM, John Stone <> wrote:

> Hi,
> The existing Windows versions of VMD are standard 32-bit builds,
> and thus they are limited to using 2GB of physical memory. It is
> possible to compile applications to use extended memory addressing
> modes that give access to about 3GB from a 32-bit app, but we haven't
> bothered with this and have instead been working on building a 64-bit
> version of VMD for Windows.
> VMD itself does compile in 64-bit Windows builds, but there had been a
> long period of problems with some of the libraries that VMD depends on.
> I've heard from at least one individual that some of these problems
> have been fixed, and so I will soon be trying to do a 64-bit build
> of VMD for Windows again.
> In the mean time, you'll have to work within the 2GB limitation,
> either by using scripts like "bigdcd" to do analysis on large
> trajectories, or by viewing subsets of your data by loading either
> a selected range of trajectory frames, or by skipping frames,
> e.g. loading only one out of every ten frames, for the purposes
> of viewing your simulation.
> I'm also working on adding support for working with out-of-core
> datasets in VMD, but this is still in the early stages and won't
> be done for some time yet.
> Cheers,
> John Stone
> On Mon, Nov 17, 2008 at 09:48:00AM -0800, wrote:
> > Hi,
> >
> > I have a general question regarding the memory use of VMD here.
> > In windows, is VMD capable of using the virtual memory or is it capable
> of
> > storing large data file temporarily in harddisk? I am using VMD for the
> > visualization of large configurations (200000 atoms in each frame,
> usually
> > more than 500 frames in total) and I just have 4GB RAM on my desktop, so
> it
> > would be a bad news for me if VMD can't use virtual memory.
> >
> > Thanks,
> >
> > Shuai
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: Phone: 217-244-3349
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