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? 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. --------------------------------------------------------------------------------------- 2) What is default value for pH in gromacs? Is pH of system during simulation constant? 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. Does the protonation of the species present in the simulation determine pH of system? 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? --------------------------------------------------------------------------------------- 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? --------------------------------------------------------------------------------------- Best wishes -- 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.
