[gmx-users] question

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================