Aw: [gmx-users] Order of atoms in topology
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! :-)
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
>>>> 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.
>>>> question is, if your topology has this, does it affect the calculations
>>>> energy or other)?*
>>> Yes, it does. For impropers, the order matters. In the two examples,
>>> 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
>>> its planarity. With "4 3 2 1," you are saying atom 4 is the planar
>>> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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