Hi Tanos, Perhaps you should try one of the available constant-pH MD methods. Here is a quick explanation of what they do and who is involved in their development right now:
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation My opinion regarding this subject may be a little biased since I've worked with one of the most active researchers in this area, but I would suggest you to read some papers from Antonio Baptista and/or Miguel Machuqueiro (from Baptista's 2002 initial "Constant-pH molecular dynamics using stochastic titration" paper to nowadays). Best regards, On Tue, May 10, 2011 at 7:22 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Tanos Celmar Costa Franca wrote: > >> >> Dear GROMACS users, >> Does someone now how to procede to change the pH of a MD simulation from >> the physiologic one (7.4) to 6.5 ? >> >> > Classical MD simulations do not currently allow for dynamic proton > exchange. The best you can do at the moment is use pdb2gmx to set the > protonation state of titratable residues. At pH 6.5, histidines will be > quite annoying to deal with properly. > > -Justin > > > >> Tanos Celmar Costa Franca - D.Sc >> Coordenador do Programa de Pos-graduacão em Química >> Secão de Engenharia Química - SE/5 >> Instituto Militar de Engenharia - IME >> Rio de Janeiro - RJ >> Brasil >> >> >> >> >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- João Henriques, MSc in Biochemistry Faculty of Science of the University of Lisbon Department of Chemistry and Biochemistry C8 Building, Room 8.5.47 Campo Grande, 1749-016 Lisbon, Portugal E-mail: joao.henriques.32...@gmail.com / jmhenriq...@fc.ul.pt http://intheochem.fc.ul.pt/members/joaoh.html
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
