[gmx-users] citation

[Justin A. Lemkul]

Elisabeth wrote:
> Hello all,
> 
> Can anyone tell me how gromacs may be cited besides
> 
> 
>       Principal Papers
> 
>    1. Berendsen, et al. (1995) /Comp. Phys. Comm./ *91: *43-56. (DOI
>       <http://dx.doi.org/doi:10.1016/0010-4655%2895%2900042-E_>,
>       Citations of this paper
>       <http://scholar.google.com/scholar?cites=6703762643559347673&hl=en>)
>    2. Lindahl, et al. (2001) /J. Mol. Model./ *7:* 306-317. (DOI
>       <http://dx.doi.org/10.1007/s008940100045>, Citations of this paper
>       <http://scholar.google.com/scholar?cites=1777735270318718960&hl=en>)
>    3. van der Spoel, et al. (2005) /J. Comput. Chem./ *26:* 1701-1718.
>       (DOI <http://dx.doi.org/10.1002/jcc.20291>, Citations of this
>       paper
>       <http://scholar.google.com/scholar?cites=8599454604037079587&hl=en>)
>    4. Hess, et al. (2008) /J. Chem. Theory Comput./ *4:* 435-447. (DOI
>       <http://dx.doi.org/10.1021/ct700301q>, Citations of this paper
>       <http://scholar.google.com/scholar?cites=15361472353040457616&hl=en>)
> 

What else are you looking for?  These are the principal papers, of which you 
should cite at least one (probably the one that pertains to the Gromacs version 
you're using).

> I am using oplsaa and found
> 
> ; References for the OPLS-AA force field:
> ;
> ; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives,
> ; J. Am. Chem. Soc. 118, 11225-11236 (1996).
> ; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998).
> ; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 
> (1998).
> ; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999).
> ; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001).
> ; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125 (2001).
> ; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen, J. 
> Phys. Chem. B 105, 6474 (2001).
> ;
> Do I have to include all these or some of them can be skipped?
> 
> Citations depend on specific features ( e.g free energy calculations, 
> ...) that have been utilized or the above references are sufficient?
> 
> Am I missing anything?

If you're not sure, you should read the papers.  Many of these pertain to 
specific functional groups and molecules that for which parameters were derived 
(see atomtypes.atp for instance).  If you did not utilize these groups, then 
citing that particular paper would be unnecessary.

-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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