From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Thu Dec 08 2005 - 15:43:28 CST

if the hbonds of interest lie on the inter-image of the PBC boxes, it
already indicates that the simulation is at risk -- proteins move
across the boundary of the box, ....

if the objects of interests are all contained in the main image, then
the suggested additions are not useful.

maybe i am missing something here?

Marc
On Dec 8, 2005, at 2:40 PM, John Stone wrote:

>
> Jerome,
> We should probably create new PBC-aware versions of the
> existing VMD functions that do:
> - 'within' and 'exwithin' atom selections
> - 'measure contacts'
> - 'measure hbonds'
> - automatic bond search (allow bonds across PBC cell boundaries)
> - draw bond components of the Bonds, CPK, and Licorice
> representations
> - draw dynamic bonds representation
>
> Adding PBC-awareness to the drawing code is the most risky in terms
> of hurting performance, but this may be something that could be dealt
> with
> by adding a checkbox so that VMD only spends effort checking for this
> when
> the user actually needs it.
>
> Before embarking on implementing all of this, it would be nice to know
> which of these users would find most beneficial. We could work on the
> most-wanted features first...
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Dec 08, 2005 at 04:03:57PM +0100, Jérôme Hénin wrote:
>> Dear VMDers,
>>
>> I suppose some of you have stumbled upon the issue of handling
>> periodic
>> boundary conditions while detecting hydrogen bonds. For instance, the
>> command
>> 'measure hbonds' is not aware of PBC, and will miss whatever bonds
>> may extend
>> across the edges of the periodic box.
>>
>> The only thing I have come up with so far is the following:
>> 1) use 'measure hbonds'
>> 2) translate a part of the system by a periodic repeat distance, so
>> that two
>> of the edges are not edges anymore
>> 3) 'measure hbonds', again
>> 4) repeat 2) and 3) until all the edges have been properly treated
>> 5) remove all the multiple-counting that we have done
>>
>> That is kind of a heavy procedure. Does anyone have a better idea?
>>
>> Thanks in advance,
>> Jerome
>>
>> --
>> Jérôme Hénin
>> Equipe de Dynamique des Assemblages Membranaires
>> Université Henri Poincaré / CNRS
>> Tel : (33) 3 83 68 43 91 Fax : (33) 3 83 68 43 87
>> http://www.edam.uhp-nancy.fr/
>
> --
> 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/ Fax: 217-244-6078
>