[gmx-users] unity in ffbonded.itp

[Justin A. Lemkul]

francesco oteri wrote:
> Dear gromacs developers,
> I would like to know what is the unity for armonic constraint in 
> ffbonded.itp. 
> In the user manual (Table 5.4) it is written that is kJ mol−1 nm−2  but 
> in the .itp file
> I read  "C  C          1     0.1525   259408.0 ; new99"

The value of 1 indicates a function type (simple harmonic expression).

> 
> I understand that 0.1525 is the equlibrium distance 5in nm) but 259408.0 
> KJ it is almost high. 
> Maybe the right value is 259408.0 J ?
> 

The quoted units are correct.  Verify yourself with the primary literature for 
the chosen force field (which may require some conversions, i.e. kcal -> kJ, 
Angstrom -> nm).

-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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