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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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