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

Mark Abraham mark.j.abraham at gmail.com
Tue Apr 30 02:34:07 CEST 2013

```I do not see that the caption to figure 4.8 implies a "reference" atom. It
talks merely about the angle between planes i-j-k and j-k-l. That angle is
signed and the sign is significant for equation 4.60. Does the sign of the
angle differ from that between l-k-j and k-j-i? I think not, but it's way
too late here for me to wrap my right-hand-rule for cross-products around
that one! :-)

Mark

On Tue, Apr 30, 2013 at 2:06 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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```