Dr. Ramón Garduño-Juárez wrote:
Hi GROMACS users,
I've two questions. My simulation box contains a DMPC lipid bilayer,
water molecules, intramembrane protein and a ligand protein. The net
charge of the system is zero. Is it necessary to add ions to this system?
A net neutral system can be simulated in the absence of any additional ions.
Counterions are principally necessary to create net neutral systems used by PME
(and also to model reality, in which no system has a net charge). The complete
absence of ions likely does not represent physical reality (and salt
concentrations do have a demonstrable effect on lipid dynamics), but it's up to
you to justify your model.
The intramembrane protein (made of two chains) has a net charge of -1
and the ligand protein has a net charge of +1, thus the net charge of zero.
The next question is too naive, but if the ions are needed, What ion is
better for the dynamics K or Na?
Neither ion is intrinsically better, but one may reflect experimental reality
better than the other. That's for you to decide.
-Justin
Much obliged.
Eduardo.
--
========================================
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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