VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.wroc.pl)
Date: Mon Dec 19 2011 - 14:42:33 CST

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
>
>