[gmx-users] reg pulling

Justin A. Lemkul jalemkul at vt.edu
Sun May 8 15:20:07 CEST 2011

vidhya sankar wrote:
> Dear justin ,
>                      Thank you for your nice reply. i am doing steered MD
> can i pulll the bonded atom ?
> by Keeping one atom reference and pulling other atom which is having 
> bond with reference atom?
> otherwise  is pull  possible only between non bonded groups?

You can pull on any atom or group that you like, in most cases, but it doesn't 
sound appropriate here.  If you pull on an atom bonded to your reference group, 
all you're going to do is cause the constraints to fail and the simulation will 
explode.  Bonds cannot break or form in classical MD, so I suppose the best 
answer to your question is that you can pull on anything you like, but the only 
interactions that can be disrupted (and keep the simulation stable) are nonbonded.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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