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.ri...@gmx.ch>
*An:* "S. Watkins" <gmx-users@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*
--
========================================
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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