VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 19 2011 - 17:21:29 CST

Can you use the "within" selection keyword to further limit it to the
waters near the site?

Cheers,
  John

On Mon, Dec 19, 2011 at 09:16:03PM +0000, Salvatore Mario Cosseddu wrote:
> Many thanks for your suggestion,
>
> But it does not apply to my case. I'm trying to make a movie of water
> molecule approaching from the bulk to a particular site, getting rid of
> H2O-OH2 bonds artificially created by dynamicBonds method. I should create
> a representation for each water approaching the site. I don't know how
> many, but they could be thousands.
>
> Thanks anyway!
> Salvatore
> On 19/12/11 20:42, Pawel Kedzierski wrote:
>
> W dniu 19.12.2011 19:08, Axel Kohlmeyer pisze:
>
> On Mon, Dec 19, 2011 at 11:44 AM, Salvatore Mario Cosseddu
> <S.M.Cosseddu_at_warwick.ac.uk> wrote:
>
> Dear all,
>
> The drawing method DynamicBonds draws bonds according to a cutoff.
>
> Let's say I have in my system the species A, B. I want to draw the
> bonds
> A-B, but I don't want B-B or A-A (even if it happens their
> distances are
> within the cutoff). What is the most clean way to do it.
>
> that is currently impossible with the DynamicsBonds representation.
>
> the only way to achieve this would be to write a Tcl procedure
> to set/delete bonds manually. not trivial, but doable. it may be
> a bit slow, if you have a lot of bonds that need to be drawn/deleted.
>
> A little better idea may be to set multiple specific DynamicBonds
> representations. For example if you want bonds A1--B1 and A2--B2 you ma
> set up two representations with separate selections A1,B1 and A2,B2.
> Bonds will be calculated within selections but not between them.
> HTH,
> Pawel
>
> cheers,
> axel.
>
> Many thanks for your help
> Salvatore
>
> --
> Salvatore Cosseddu
> PhD student
>
> Centre for Scientific Computing and School of Engineering
> University of Warwick
> Coventry CV4 7AL
> United Kingdom
>
> email: S.M.Cosseddu_at_warwick.ac.uk
>
> --
> Salvatore Cosseddu
> PhD student
>
> Centre for Scientific Computing and School of Engineering
> University of Warwick
> Coventry CV4 7AL
> United Kingdom
>
> email: S.M.Cosseddu_at_warwick.ac.uk 

-- 
NIH Resource 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/       Fax: 217-244-6078