[gmx-users] question

[Andrew Bostick]

Hi gmx users

I am beginner in gromacs. Excuse me for my simple and ordinary questions.
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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.
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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?
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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?
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Best wishes