[gmx-developers] pull code generalization feedback request

[XAvier Periole]

The dimensions we use to define the relative orientation of two objects are defined using three anchors on each object (A,B,C) and (a,b,c). It is easier to place them on a equilateral triangle: 
- the distance between the centres of masses (anchors A and a) of the two objects: d(A,a),
- the second and third ones are the bond angles between the vector defined by the centres of masses (A and a) and the second anchor point (B and b): <Aab and aAB.
- the forth is the dihedral angle around the Aa vector: [BAab
- the last two are rotations around the objects themselves: [Abcd and [aBCD

Each of these dimensions are independent and may vary independently, that is actually the all point of it :)

I hope this is more clear if not ask again :))

On Oct 21, 2013, at 5:37 PM, "Shirts, Michael (mrs5pt)" <mrs5pt at eservices.virginia.edu> wrote:

> Hi, Xavier-
> 
>> I realise that this is a bit late but it would be really great to be able to
>> include multi-dimensional umbrella sampling with the option to define multiple
>> bonds, angles and dihedrals simultaneously.
> 
> Can you define "multi-dimensional" in this context?  If the bond, angles,
> and dihedrals are defined simultaneously, then isn't there just one
> dimension?  What is the second dimension?
> 
> It's possible some of this can be done now, actually, depending on what you
> mean. But if you can be more clear as to exactly what the dimensions you
> want to simulate now, and how you code the restraints in currently, then it
> will be very straightforward to include such functionality in what is
> already planned for 5.0.
> 
> Best,
> ~~~~~~~~~~~~
> Michael Shirts
> Assistant Professor
> Department of Chemical Engineering
> University of Virginia
> michael.shirts at virginia.edu
> (434)-243-1821
> 
> 
> 
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