[gmx-users] Charge groups

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> Dear All
> 
> I read charge groups section in the gromacs manual.
> I have a question.please let me know it's answer.
> 
> Is it necessary that our charge groups be made of afew number of atoms?
> in the other words ,if I have a charge group with 50 atom,Is my results 
> valid?

Absolutely not.  Short-range Coulombic interactions are based on the centers of 
charge groups falling within the cutoffs specified in the .mdp file.  With a 
charge group of 50 atoms, you'll be missing countless interactions.

> I didn't see anywhere in manual to dertermine any extent for number of 
> atoms in charge groups!

See examples in the .rtp file and in the primary literature for the force field 
of interest.

> It had just noticed we must make charge groups for atoms with total 
> charge of zero,atoms near to eachother in position.
> 

Charge groups do not have to have zero charge.  They usually have integral 
charge, but if you're going to be using PME, this is not an absolute requirement.

-Justin

> Thanks in advance
> Mohsen
> 

-- 
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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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