VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Sun May 11 2008 - 12:35:35 CDT

Hi John and Axel,

Thanks for the answer. Where is the 'pbcwithin' command available? (1.8.7 is
not out yet, right?)
-Neelanjana

On Sun, May 11, 2008 at 8:54 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> We have a new "pbcwithin" command in the test builds of VMD 1.8.7
> if you would like to try it, but the normal "within" command found
> in older versions doesn't take PBC into account.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, May 11, 2008 at 12:04:57AM -0700, Neelanjana Sengupta wrote:
> > Dear VMD users,
> >
> > Can anybody ascertain if the 'within' command takes into account periodic
> > boundary conditions? In other words, for obtaining the atoms 'within' a
> > certain distance of a selection, is the distance between the selection
> and
> > each atom recalculated as:
> > dx=dx - cell_a*NINT(dx/cell_a), etc?
> >
> > This is for a dcd file where the unit cell dimensions are specified at
> each
> > step.
> >
> > Thanks,
> > Neelanjana Sengupta
> > --
>
> --
> 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: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

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