[gmx-users] Charmm force field with gromacs

[Justin A. Lemkul]

Lennart Nilsson wrote:
> Hi Justin,
> 
>  
> 
> In brief:
> 
> In practice there is only one CHARMM forcefield - all components work 
> together;  the components happen to have numbers corresponding to the 
>  most recent version of CHARMM at the time this particular component was 
> produced. The lipid and sugar components of the forcefield have, quite 
> naturally, been evolving more rapidly than the protein (stable since 
> ~1993) and nucleic acid (stable since ~2000) components. So, CHARMM22 
> for proteins and CHARMM27 for nucleic acids refer to different 
> components of the SAME forcefield.  There is also an older protein 
> forcefield, CHARMM19, which is not all-atom.
> 
>  
> 
> I hope that the crew who ported the CHARMM forcefield to GROMACS 
> understands this.
> 

Thanks for the explanation.  I'm sure the developers knew what they were doing, 
and hopefully my inarticulate reply doesn't cause anyone to question their 
knowledge.  What I was hoping to make clear was that any user searching for a 
specific force field should simply be aware of what they're actually using.  The 
Perl scripts contributed to Gromacs worked with a few parameter sets several 
years ago, and the git code provides CHARMM27 so the two approaches proposed in 
the original post do not correspond to strictly the same result.  Generic 
terminology is all too often thrown around, even in the literature 
unfortunately, like "we used the Gromos force field" or "the standard Gromacs 
force field," a term which is very misleading.  In hoping to enlighten someone 
else, I too have been duly informed :)

-Justin

>  
> 
> Best wishes,
> 
> Lennart Nilsson
> 

-- 
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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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