If you want Zn2+ ions to actually do something useful then rather than just balance the charges you might want more of them - otherwise they might just diffuse around. You could use the -conc flag with the -neutral flag.
> > > On 12/5/13 6:10 AM, Andrew Bostick wrote: >> Hi gmx users >> >> I am beginner in gromacs. Excuse me for my simple and ordinary >> questions. >> --------------------------------------------------------------------------------------- >> >> 1) In the most of tutorials and papers I read to now, for the simulation >> of >> a protein >> with a net charge (for example: -5 e) in aqueous solution, counterions >> (in this case: 5 Na ions) are added to neutralize the system. I have a >> question about >> that. Is neutralization of the system prior to md simulation mandatory >> in >> the gromacs? >> > > Neutralization of a system is not decided based on the software, it is > decided > based on the algorithms used and what they require; that's true of any MD > program. The short answer is: it depends on what you are doing. This > topic has > been discussed extensively on the mailing list, even in recent days. > Google is > your friend. > >> If I want to do md simulation of my protein in the presence of Zn2+ >> ions, >> How to >> manage both of (a) neutralize the system and (b) addition of specific >> concentration >> or number of Zn2+ ions (for example: 3 zinc ions) simultaneously? >> >> I know using [genion -s ions.tpr -o system.gro -p topol.top -np 5 -pname >> NA >> -pq +1] >> is true for (a). But for (b), I have not opinion. > > If the ions are a necessary component of the system, that simply changes > the net > charge of the system. If the protein is -5 e and the ions sum to +6 e, > then > your solute has a net charge of +1 e. You can easily add the 3 Zn2+ and 1 > Cl- > (or whatever else) counterion in one genion command. > >> --------------------------------------------------------------------------------------- >> >> 2) What is default value for pH in gromacs? Is pH of system during >> simulation constant? > > There is no default pH. Given that there are no exchangeable protons in a > classical MD simulation, the protonation states of whatever molecules you > have > are chosen by you. Titratable residues can be adjusted with relevant > pdb2gmx > command-line options. > >> Can I change pH value in mdp file? On the other hand, can I study 3 md >> simulations with >> 3 different pH (4.5, 7, 9.5)? I did not find issue about pH in chapter 7 >> of >> the manual. >> > > There is no .mdp option for this; it is a function of the topology and is > set > when running pdb2gmx. You need to know the pKa values of all the > titratable > residues and set their protonation states accordingly. One cannot really > argue > that you are doing a simulation at any pH value at all, but you are > instead > simulating the dominant species that would occur in a solution at that pH. > >> Does the protonation of the species present in the simulation determine >> pH >> of system? >> > > Not according to the standard definition of what pH is. There are no > hydronium > ions in the system, and even if there were, they can't behave in any > realistic > way in a classical simulation. > >> For example, if I have 3 lysine in my protein and N-terminal and >> C-terminal >> be NH3+ and >> COO-, respectively, pH for my system will be 3? > > That would be a false statement. Net charge and pH are not equivalent. > >> --------------------------------------------------------------------------------------- >> >> 3) In some pdb files, there are missing atoms or missing residues. If I >> want to not use >> -missing option of pdb2gmx and missing atoms or missing residues be very >> important in my >> study, is there a way to obtain this missing atoms or missing residues? > > There are many modeling programs and even some web servers that will > rebuild > missing atoms, residues, or loops. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > 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. > -- 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.