[gmx-users] problem in oplsaa ffbonded.itp

[Justin A. Lemkul]

francesco oteri wrote:
> Dear Gromacs users,
> I am working on a program that need topology parsing. 
> I am using the OPLSAA forcefield and I noticed that in ffbonded.itp file 
> belonging to this force field there are these strange lines:
> 
> [ dihedraltypes ]
> ;  i    j    k    l   func     coefficients
> ; Added DvdS for Quartz simulations
>    SI   OS    1     0.000       3.766      3
>    SI   OH    1     0.000       3.766      3
> 
> 
> If it describes dihedral definition, how is possible having only two 
> atom types?
> 

Those are the central two atoms in the dihedral, i.e. atoms j and k in the 
i-j-k-l notation for a dihedral.

-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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