[gmx-users] question

[jkrieger at mrc-lmb.cam.ac.uk]

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