Aw: [gmx-users] Order of atoms in topology

[Mark Abraham]

On Mon, Apr 29, 2013 at 11:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
> Please start a new thread if you're going to introduce a new topic.  I
> have changed the subject to something more relevant.
>
> On 4/29/13 4:23 PM, lloyd riggs wrote:
>
>> *Dear All,*
>> *Doing a water/temp energy minimization just for a figure with a large
>> molecule
>> that has several connected parts, I ran into a bizzar question.*
>> *So I found its possible by accident to define improper dihedrails
>> forwards and
>> backwards without gromacs complaining, such as atom 1 2 3 4 and 4 3 2 1.
>>  My
>> question is, if your topology has this, does it affect the calculations
>> (angle
>> energy or other)?*
>>
>
> Yes, it does.  For impropers, the order matters.  In the two examples, you
> are specifying different properties.  With "1 2 3 4," you are saying that
> atom 1 is planar and atoms 2, 3, and 4 are the atoms around it that govern
> its planarity.  With "4 3 2 1," you are saying atom 4 is the planar center,
> with atoms 1, 2, and 3 similarly governing its planarity.
>

I didn't know that. A quick look in the manual didn't reveal where we have
that documented. Do we?

(Obviously, it is only applicable to harmonic-type improper dihedrals.)

Mark