Aw: [gmx-users] Re: how is the pulling force measured

[Justin Lemkul]

On 4/30/13 12:33 PM, lloyd riggs wrote:
> I appologise, I meant defined at the same time without complaining, not just
> either direction.

A different atom order is interpreted as a different interaction.  In this case, 
if both are defined, there is indeed a difference in the improper energy term. 
I have a toy test case that shows this.

-Justin

> *Gesendet:* Montag, 29. April 2013 um 22:23 Uhr
> *Von:* "lloyd riggs" <lloyd.riggs at gmx.ch>
> *An:* "S. Watkins" <gmx-users at gromacs.org>
> *Betreff:* Aw: [gmx-users] Re: how is the pulling force measured
> *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)?*
> *Stephan Watkins*
>
>

-- 
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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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