[gmx-users] Charge groups

Justin A. Lemkul jalemkul at vt.edu
Sun Feb 6 14:04:02 CET 2011

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.


> Thanks in advance
> Mohsen


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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