VMD-L Mailing List

From: Salvatore Mario Cosseddu (S.M.Cosseddu_at_warwick.ac.uk)
Date: Mon Dec 19 2011 - 15:16:03 CST

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, Paweł Kędzierski 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