[gmx-users] Constraints for md simulations of carbohydrates

[Justin A. Lemkul]

Neha Bharat Gajaria wrote:
> Dear List,
> 
> I want to study the ring puckering of carbohydrates. Is it recommended 
> to use hydrogen-bond constraints or i simply put none in constraints 
> section in the md.mdp file?

That depends on the time step you want to use.  Refer to the LINCS references 
provided in the manual.

-Justin

> 
> Many thanks,
> 
> Regards,
> Neha Gandhi Gajaria,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
> 

-- 
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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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