[gmx-users] Bonds definition in itp files

[Justin Lemkul]

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 <jalemkul at 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
>>
>> --
>> ==================================================
>>
>> 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
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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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

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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