[gmx-users] Too many parameters in itp-file

[Justin A. Lemkul]

Mikkel Vestergaard wrote:
> Hi,
> I have used an itp file which include following lines:
> [constraints]
> ;  i     j   funct   length
> ;   1     2    1       0.14
> ;   1     3    1       0.14
> 
> ; for minimization purposes replace constraints by stiff bonds:
> ;
> ;[bonds]
> ;  i     j   funct   length   force const.
>    1     2    1       0.14    50000
>    1     3    1       0.14    50000
> 
> 
> 
> 
> It was intended to look like this (other lines commented out):
> [constraints]
> ;  i     j   funct   length
>    1     2    1       0.14
>    1     3    1       0.14
> 
> ; for minimization purposes replace constraints by stiff bonds:
> ;
> ;[bonds]
> ;  i     j   funct   length   force const.
> ;   1     2    1       0.14    50000
> ;   1     3    1       0.14    50000
> 
> So the only difference from the intended lines was the extra parameter 
> 50000. Does Gromacs use the extra parameter for something or is it just 
> ignored? (Got no warnings in simulations.)
> 

The functional forms for harmonic bonds are given in the manual.  The force 
constant is used in this case, if constraints are not.

-Justin

> Thanks,
> Mikkel
> 

-- 
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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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