The standard procedure of H+ interchange and transition states can be done through QM/MM. Please give one reference according to the algorithms you have mentioned.
Cheers. >>> João M. Damas 06.09.11 15.19 Uhr >>> As Justin said, constant protonation != constant pH. Constant-pH MD does not simulate H+, but allows changes in protonation states during the MD simulation. There are different algorithms to accomplish that. Cheers, João On Tue, Sep 6, 2011 at 2:04 PM, Emanuel Peter <emanuel.pe...@chemie.uni-regensburg.de> wrote: Could you just tell me smth. ! No forcefield on whole earth is able to reproduce the pH realistically by H+. You just can apply pH of your system through the protonation states of each part in your system. monkey. >>> João M. Damas 06.09.11 14.22 Uhr >>> That is not considered constant-pH MD. Follow Justin's suggestion. Cheers, João On Tue, Sep 6, 2011 at 12:47 PM, Emanuel Peter <emanuel.pe...@chemie.uni-regensburg.de> wrote: Look for the pKa-constants of each part of your system (e.g. each amino-acid). Then you can check each protonation state and change it according to your application in the force-field. Emanuel >>> fancy2012 06.09.11 13.01 Uhr >>> Dear gmx users, Are there some tutorials on constant PH simulations using gromacs? How should I state my work? Right now I have no idea on it. -- Best wishes, Qinghua Liao Ph.D student of Tianjin University, China -- 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 M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613 -- 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 M. Damas PhD Student Protein Modelling Group ITQB-UNL, Oeiras, Portugal Tel:+351-214469613
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