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

Justin Lemkul jalemkul at vt.edu
Tue Apr 30 02:06:36 CEST 2013

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On 4/29/13 8:00 PM, Mark Abraham wrote:
> 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.)
>

I have always interpreted Figure 4.8 to imply that if one changes the order of
the atoms (ai, aj, ak, al in the topology), the planes defined around the
reference atom would be different for a given set of 4 atoms in different order.
Is this not the case?  I haven't gone into the code to see how the topology is
interpreted.

-Justin

--
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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