On 11/4/16 6:09 PM, Alex wrote:
Dear gromacs user, In my simulation (solid surface + peptide in aqueous solution) I have a heptpeptide in which contains 2 times Glutamic acid (negatively charged) and one Arginine(positively charge) and one Lysine(positively charge), so, as you see the heptpeptide is charge neutral in general(the whole system is also neutral) despite having charged amino acid. However, In such situation I see sometimes people add also "Na + Cl" as counter-ion in the system, I do not know why!, I was wondering if it is really necessary to do that or make sense, as It is neutral initially? What if I do not add them? How can I see their effects quantitatively? How can I find out if I need the Counter-ions or not?
Counterions and bulk salt are different. A counterion is specifically added to balance the net charge on the solute. If the solute is neutral, no ions that are added into the bulk are counterions. They are all bulk ions that are part of the ionic environment in the system. People do this to mimic experimental or physiological conditions, because ions increase the dielectric of the solution and screen charges.
-Justin
By, the way, the goal of simulation is to calculate the PMF of heptapeptide-surface interaction* in *physiological condition by US. Thanks in advance. Regards, Alex
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
