[gmx-users] NaCl

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:
> 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.
> 

There may be information from solid-state crystals, but as far as an aqueous 
solution goes, Mark is quite right - this is not a relevant state for NaCl in 
water.  There is no appreciable quantity of un-ionized NaCl in water, so that's 
why you're probably going to find it difficult to find bond parameters that are 
compatible with OPLS-AA.

-Justin

> 
> 
> 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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> 
> 
> 

-- 
========================================

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

========================================