Aw: [gmx-users] Order of atoms in topology
jalemkul at vt.edu
Tue Apr 30 03:19:11 CEST 2013
On 4/29/13 8:34 PM, Mark Abraham wrote:
> I do not see that the caption to figure 4.8 implies a "reference" atom. It
Sorry, loose terminology after a long day. "Reference atom" is a poor choice.
What I meant was with respect to the way pdb2gmx constructs impropers - the
central atom (i.e. the one around which planar geometry is to be observed) is
written first as atom i.
> 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! :-)
I created a simple test case that confirms that for _exact reversals_ of atom
numbers within an improper listing (i.e. 1 2 3 4 vs. 4 3 2 1), the energy
associated with the improper term does not differ significantly. Minor
differences noted, but within error, hence standard MD at play :) For any other
order, things go haywire.
> 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
>> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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