[gmx-users] simulation at particular pH
g.groenhof at rug.nl
Tue Aug 8 22:15:40 CEST 2006
Bad idea. Adding just one proton (1/Navogadro moles ~ 1.6 * 10^-24)to a
box of say 500 nm^3 (5 10^-22 liter), continaining roughly 10000 waters
would give a pH of 2.5 (-log[1.6/5*10^-2), which is the maximum pH you
can reach for such standard box. If you want to go higher, say to pH=7,
your box needs to be at least 1.6 * 10^-17 liter, or 1.6 * 10^7 nm^3.
THis is too big for simulation.
Therefore adding H+ or H3O+ is not really an option. Instead you should
choose the protonation states of the titrating sites in the system such
that they correspond to the pH your are interested in. Equilibrium
exchange of protons between aminoacid sidechains is probably happening
on a timescale much longer than a typical simulation length.
On Aug 8, 2006, at 9:16 PM, Arthur Roberts wrote:
> Hi, Luisa,
> I would first calculate the number of protons (H+)
> that you would find your water box. Then I would use
> the command genion to generate that number of H+'s
> that corresponds to the pH. Then I would use grompp
> to find out what the final charge is. If it is still
> negative, I would add NA+. If it is positive, I would
> add CL-. This should approximate the pH. Although
> there is one problem, ionizable residues. You will
> need to set those manually. I am not sure, if you can
> use the morse potential on specific residues instead
> of harmonic potential to make a residue ionizable. I
> hope this helps.
> Best wishes,
> Art Roberts
> University of Washington
> Department of Medicinal Chemistry
> --- luisa pugliese
> <luisa.pugliese at safan-bioinformatics.it> wrote:
>> Hello to everybody,
>> I am new to this mailing list and I am writing
>> because I wonder if anybody knows how can I set up
>> the pH of the system in gramacs.
>> Thank you to everybody
>> Luisa Pugliese, Ph.D.
>> luisa.pugliese at safan-bioinformatics.it
>> S.A.F.AN. BIOINFORMATICS
>> Corso Tazzoli 215/13 -10137 Torino - ITALY
>> tel +39 011 3026230
>> fax +39 011 3165080
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