Molecular simulations in Breve

Hi,

We just recently began using the Breve program here at our research lab. We 
are trying to write a simulation based on protein interactions. Basically, 
what we are trying to do is simulate the formation of  a lipid bilayer 
protein on a 2-dimensional surface. Currently we are having problems with 
the collisions of the spheres (molecules), we want them to be able to bounce 
off each other rather than merge. We were looking at modifying the default 
included demos to suit our needs, however it is proving unsuccessful.  Do 
you have anymore literature or documentation regarding the simulations? Or 
how about a tutorial on how to create a molecule based simulation.

Regards and Thank you for your time,

Cindy Chan

>From: [email protected]
>Reply-To: [email protected]
>To: [email protected]
>Subject: breve Digest, Vol 16, Issue 3
>Date: Wed, 17 Nov 2004 12:00:22 -0500 (EST)
>
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>Today's Topics:
>
>    1. mailing list (Cindy Chan)
>    2. Newbie Joint question (Jon Kleiser)
>    3. Light Exposure (Nicolas Lassabe)
>    4. Re: Light Exposure (jon klein)
>    5. Re: Newbie Joint question (jon klein)
>    6. Re: Light Exposure (lassabe)
>    7. Re: Light Exposure (jon klein)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 16 Nov 2004 20:43:10 -0500
>From: "Cindy Chan" <[email protected]>
>Subject: [breve] mailing list
>To: [email protected]
>Message-ID: <[email protected]>
>Content-Type: text/plain; charset="us-ascii"
>
>An HTML attachment was scrubbed...
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>------------------------------
>
>Message: 2
>Date: Wed, 17 Nov 2004 11:15:17 +0100
>From: Jon Kleiser <[email protected]>
>Subject: [breve] Newbie Joint question
>To: [email protected]
>Message-ID: <p05200f01bdc0ce461ffb@[129.240.92.62]>
>Content-Type: text/plain; charset="us-ascii" ; 
format="flowed"
>
>Hello,
>
>I'v just put together my first breve simulation: A MultiBody
>consisting of two pyramides hinged together by a RevoluteJoint. The
>two pyramides are instances of the same CustomShape. If I don't
>connect the pyramides, I can rotate them independantly, but the
>moment I apply the joint this rotation seems to be forgotten, and
>they melt together into one pyramide, until the velocity of the joint
>moves them apart. How can I hinge together two bodies (of the same
>shape) without disturbing their orientation? Is it possible to have a
>RevoluteJoint that is totally passive (initially)?
>
>I plan to connect several pyramides, in a ring, if this works well ;-)
>
>Sincerely,
>
>Jon Kleiser
>--
>
>------------------------------
>
>Message: 3
>Date: Wed, 17 Nov 2004 13:40:37 +0100
>From: Nicolas Lassabe <[email protected]>
>Subject: [breve] Light Exposure
>To: [email protected]
>Message-ID: <[email protected]>
>Content-Type: text/plain; charset="iso-8859-1"
>
>I would like to use LightExposure function in my simulations. The
>function always returns 0. I use enable-light-exposure-detection
><http://www.spiderland.org/breve/breve_docs/classes/Control.html#enable-light-exposure-detection>
>and get-light-exposure.  If an object is in the shadow of anothre one,
>the ligth exposure will be less ???
>
>
>Thanks,
>
>Nicolas*
>*
>-------------- next part --------------
>@use Stationary.
>@use PhysicalControl.
>@use Mobile.
>
>Controller Exposure.
>
>PhysicalControl : Exposure {
>	+ variables:
>		floor (object).
>		floorShape (object).
>     + to init:
>   		self enable-shadow-volumes.
>
>		self point-camera at (0, 0, 0) from (19, 30, 34).
>		floorShape = (new Shape init-with-cube size (1000,1,1000) ).
>		floor = new Stationary.
>		floor register with-shape floorShape at-location (0, 0, 0).
>		#floor set-color to (1, 1, 1).
>		self enable-lighting.
>		self enable-light-exposure-detection.
>		self set-light-exposure-source to (0,50,0).
>
>		self drop-cube.
>
>	+ to drop-Cube:
>		new Cube.
>}
>
>Mobile : Cube {
>	+ to init:
>		self set-shape to (new Cube init-with size (10,10,10)).
>		self set-color to (1, 0, 1).
>		self move to (0,40,0).
>		self enable-physics.
>	+ to iterate:
>		print (self get-light-exposure).
>
>
>}
>
>------------------------------
>
>Message: 4
>Date: Wed, 17 Nov 2004 08:36:40 -0500
>From: jon klein <[email protected]>
>Subject: Re: [breve] Light Exposure
>To: [email protected]
>Message-ID: <[email protected]>
>Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
>
>On Nov 17, 2004, at 7:40 AM, Nicolas Lassabe wrote:
>
> > I would like to use LightExposure function in my simulations. The
> > function always returns 0. I use enable-light-exposure-detection
> > <http://www.spiderland.org/breve/breve_docs/classes/
> > Control.html#enable-light-exposure-detection> and 
get-light-exposure.
> > If an object is in the shadow of anothre one, the ligth exposure 
will
> > be less ???
>
>I recently discovered that light exposure is mostly not working in
>breve 2.0, but the problem has been fixed for the next release.  If
>you'd like a development build of 2.1 which fixes the problem, let me
>know.
>
>- jon klein
>
>
>------------------------------
>
>Message: 5
>Date: Wed, 17 Nov 2004 08:40:17 -0500
>From: jon klein <[email protected]>
>Subject: Re: [breve] Newbie Joint question
>To: [email protected]
>Message-ID: <[email protected]>
>Content-Type: text/plain; charset=US-ASCII; format=flowed
>
>
>On Nov 17, 2004, at 5:15 AM, Jon Kleiser wrote:
>
> > Hello,
> >
> > I'v just put together my first breve simulation: A MultiBody
> > consisting of two pyramides hinged together by a RevoluteJoint. 
The
> > two pyramides are instances of the same CustomShape. If I don't
> > connect the pyramides, I can rotate them independantly, but the 
moment
> > I apply the joint this rotation seems to be forgotten, and they 
melt
> > together into one pyramide, until the velocity of the joint moves 
them
> > apart. How can I hinge together two bodies (of the same shape) 
without
> > disturbing their orientation? Is it possible to have a 
RevoluteJoint
> > that is totally passive (initially)?
>
>The relative positions and rotations of objects in the world do not get
>used when the objects are linked.  Instead, this information is handled
>by the joint.  So instead of setting their rotation in the real world
>and then linking them, you need to tell the Joint itself what kind of
>rotation you'd like.
>
>Have a look at the Joint methods set-relative-rotation and
>set-relative-rotation-matrix.
>
>- jon klein
>
>
>------------------------------
>
>Message: 6
>Date: Wed, 17 Nov 2004 14:54:43 +0100
>From: lassabe <[email protected]>
>Subject: Re: [breve] Light Exposure
>To: [email protected]
>Message-ID: <[email protected]>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>Don't worry, I will wait the version 2.1.  I would like just to know if
>an object is in the shadow of anothre one, the ligth exposure will  be
>less ???
>Thanks,
>Nicolas
>
>jon klein wrote:
>
> >
> > On Nov 17, 2004, at 7:40 AM, Nicolas Lassabe wrote:
> >
> >> I would like to use LightExposure function in my simulations. 
The
> >> function always returns 0. I use 
enable-light-exposure-detection
> >> <http://www.spiderland.org/breve/breve_docs/classes/
> >> Control.html#enable-light-exposure-detection> and
> >> get-light-exposure.   If an object is in the shadow of anothre 
one,
> >> the ligth exposure will  be less ???
> >
> >
> > I recently discovered that light exposure is mostly not working in
> > breve 2.0, but the problem has been fixed for the next release.  
If
> > you'd like a development build of 2.1 which fixes the problem, let 
me
> > know.
> >
> > - jon klein
> >
> > _______________________________________________
> > breve mailing list
> > [email protected]
> > http://lists.spiderland.org/mailman/listinfo/breve
> >
> >
>
>
>------------------------------
>
>Message: 7
>Date: Wed, 17 Nov 2004 08:57:25 -0500
>From: jon klein <[email protected]>
>Subject: Re: [breve] Light Exposure
>To: [email protected]
>Message-ID: <[email protected]>
>Content-Type: text/plain; charset=US-ASCII; format=flowed
>
>
>On Nov 17, 2004, at 8:54 AM, lassabe wrote:
>
> > Don't worry, I will wait the version 2.1.  I would like just to 
know
> > if an object is in the shadow of anothre one, the ligth exposure 
will
> > be less ???
>
>Yes -- light exposure works by assigning exposure values based on the
>surface area visible from the perspective of the sun.
>
>- jon klein
>
>
>------------------------------
>
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>
>
>End of breve Digest, Vol 16, Issue 3
>************************************


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