[gmx-users] NaCl

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 16 20:00:00 CEST 2010

nishap.patel at utoronto.ca wrote:
> Hello,
>     I want to simulate a simple NaCl ion in water. I know the method 
> using genion which adds individual Na+ and Cl- ion, but I wish to 
> simulate Na-Cl connected rather than free ions floating in water. When I 
> ran the grompp command I got the error:
> No default Bond types
> So I am thinking, I need to add b0 and Kb values for NaCl? Is that correct?
> I would really appreciate some help!

This really is a case where you can try it and see much faster than it will take 
you to type the email asking for help :)

Presumably, if you want a bond, and there are not parameters for it already 
built in, then yes, you need to actually define the bond.


> Thanks.
> -Nisha P


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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