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

Justin Lemkul jalemkul at
Mon Apr 29 23:34:27 CEST 2013

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.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at] | (540) 231-9080


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