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?
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 -- 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.
