If I'm right, the only sense of order mattering is that the forces are
different in the instant, but no matter what the shape of the energy
well that bottoms at planarity, it is merely an artifact of the force
field, and one shape is no more correct than another. And random
ordering might be better scientifically as a result, except that it
would affect exact repro of results.
The only reasons I remember for fixing the order is so that test diffs
of prmtop internal order and test energies don't diverge.
Bill
On 3/24/16 3:40 PM, David Cerutti wrote:
> For Bill's question, my supposition would be that order doesn't matter so
> long as the angles between all atoms around the improper are precisely 120.
> But, even if those are the equilibria the precise positioning in a
> simulation will not be.
>
> Here's what I'm doing, over the quizzical looks from my officemate. Put
> your arm flat on a high table so your humerus is in the plane of the
> tabletop. Your elbow is point "C", the center of the improper, your
> shoulder is point A, your hand point B, and place a coffee cup on the table
> as point D. Put your elbow at 120 degrees, so the A-C-B angle is 120.
> Rotate your arm so that your shoulder and elbow stay in the plane of the
> table but your hand lifts off. That's bending between A-C-B and A-C-D.
> Now extend your elbow outwards until your hand is nearly straight. The
> angle between the A-C-B and A-C-D planes is not changing, but visualize the
> plane of B-C-D. The incline of the B-C-D plane is changing despite the
> fact that the incline of A-C-B is not, and the A-C-D plane is, as always,
> in the plane of the table. That's my thought experiment to convince myself
> that the order of atoms in impropers matters, but perhaps only in the limit
> of significant departures from planarity.
>
> I just spilled my coffee.
>
>
> On Thu, Mar 24, 2016 at 3:24 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> David, why does the order matter, aside from consistency, as long as the
>> function is planar, and possibly the central atom is in position 2 or 3?
>> My impression is that if you randomly assigned atoms for each improper
>> and ran a long enough simulation, the ensembles would converge. (Bearing
>> in mind that impropers seem like a somewhat hacky way of enforcing
>> planarity in the first place.)
>>
>> Regards,
>> Bill
>>
>> On 3/24/16 4:23 AM, David A Case wrote:
>>>> 2.) Can anyone confirm that, for any atom types A, B, and D, an
>> improper A
>>>>> B C D is equivalent to an improper D B C A and also B D C A, or any
>> other
>>>>> permutation that leaves C in position 3?
>>> Above is wrong: the fact that the order of A,B and D matters is the
>> origin of
>>> requiring them to be an alphabetical order. The only invariant thing
>> you can
>>> do with a torsion (proper or improper) is to reverse it: ABCD == DCBA.
>> All
>>> other permutations are different.
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 24 2016 - 19:00:04 PDT
