VMD-L Mailing List

From: Bishop, Thomas C (bishop_at_tulane.edu)
Date: Thu Aug 13 2009 - 14:46:24 CDT

NOTE also that VMD is a display program rather than a computation engine.
During a molecular dynamics periodic images certainly interact
and chemical bonds can be setup to extend across the entire length of the periodic cell s.t.
the bond really just passes thru the wall of the periodic cell.

VMD will display these bonds as extending across the entire cell but NAMD will calculate them as shortest distance.

So for instance you can have an "infinitely" long nanotube or piece of DNA.

I utilized such periodic chemical structures (PCS) in Bishop, JBSD v22, 2005 and
Zhmudsky, Cortez, Bishop J. Comp. Phys 2004.
There are some consequences to be aware of but it works.
This is one way to get rid of "END" effects like fraying of ends of free DNA or end effects that affect ion distribution.

Tom

 

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu on behalf of Axel Kohlmeyer
Sent: Wed 8/12/2009 9:42 AM
To: Liang, Linus H.
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Periodic Bonding
 
On Wed, Aug 12, 2009 at 9:44 AM, Liang, Linus H.<lianglh_at_ornl.gov> wrote:
>
> Dear all,
>
> I know it is possible to display periodic images, but is it possible to allow the periodic representations to interact with the original representation .

no. the periodicity display is generated _after_ the bonding is established.
this topic has come up many times here, but the solution is not easy.

axel.

> Thanks,
>
> Linus
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.