[gmx-users] simulation at particular pH

[Marc Baaden]

Hi,

I would like to add a little nuance to Gerrit's answer. Although he is right
that there is currently no way of accurately and generally modeling acidity
by introducing explicit H3O+/OH-, one can still use that approach to check
the groce effect in benign cases, like eg if you were to investigate an
industrial process at 1 M acid. At least we tried so in the past [1] and got
some interesting results.

Marc

[1] TBP at the water - oil interface: the effect of TBP concentration and
    water acidity investigated by molecular dynamics simulations
    J. Phys. Chem. B, 105, 2001, 11131-11141

>>> Gerrit Groenhof said:
 >> 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.
 >> 
 >> Gerrit
-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
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