nishap.pa...@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" <jalem...@vt.edu>:
nishap.pa...@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
========================================
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