[gmx-users] NaCl

[nishap.patel at utoronto.ca]

I believe the bonds are not defined in the OPLS-AA force field for  
NaCl. I know this might sound like a stupid question, but is there a  
way to determine the bond force constant (kb), I tried to look it up,  
but I couldn't find anything.



Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> 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.
>
> -Justin
>
>>
>> Thanks.
>>
>> -Nisha P
>>
>>
>
> -- 
> ========================================
>
> 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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