Justin A. Lemkul
jalemkul at vt.edu
Mon Aug 16 22:51:29 CEST 2010
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.
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>> nishap.patel at utoronto.ca wrote:
>>> 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
>>> 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.
>>> -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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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