On 4/6/20 9:55 AM, Sina Omrani wrote:
Thanks, dear Justin. if I define a constraint on a bond then force constant
isn't useless?
Yes, because you no longer have a harmonic interaction. It is a fixed
length. Whether or not the bond should be constrained is dictated by
whether or not the force field applies constraints to all bonds or only
bonds to H. If the latter, you shouldn't apply ad hoc constraints.
-Justin
On Mon, 6 Apr 2020 at 17:12, Justin Lemkul <jalem...@vt.edu> wrote:
On 4/6/20 7:24 AM, Sina Omrani wrote:
Hi,
I wanted to know how we specify a bond order in our simulation? For
example, if we have a triple bond in our structure between atoms 1 and 2,
is it by length and force constants or we define 1 and 2 bonds three
times
in the bond section of itp file?
What if we use a constraint on this bond? because I get better results
when
I define the bond three times but haven't seen this method. is it wrong?
All interactions should be defined only once, and the parameters used
should produce correct behavior. MM force fields have no concept of
double or triple bonds; they only know the stiffness of the spring
connecting the atoms. My guess is that if you had to add the bond three
times, the force field parameters are adding together, indicating that
the force constant is unsuitable for what you're trying to and needs to
be refined.
-Justin
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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