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
--
========================================
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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