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:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php