[gmx-users] simulation at particular pH
baaden at smplinux.de
Wed Aug 9 10:33:51 CEST 2006
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  and got
some interesting results.
 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.
Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
mailto:baaden at smplinux.de - http://www.baaden.ibpc.fr
FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
More information about the gromacs.org_gmx-users