There is documentation on this at http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation but the link to the mailing list there is out of date.
Also what about the method of Lee et al., J. Chem. Theory Comput., 2014 ( http://pubs.acs.org/doi/full/10.1021/ct500175m )? I guess once Enveloping Distribution Sampling is implemented (Michael Shirts was planning this for 5.2 in Nov 2014: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-November/008100.html ) then protonation with HREx and EDS could follow. Not being at all involving in any developing myself I don't know how feasible this is or how long it would take. Best wishes James > > > On 12/20/15 11:36 PM, Sana Saeed wrote: >> hi gmx usershow would i know the PH of the system, and how to manage the >> value of PH, WHAT should i CHANGE to simulate a system at PH =2 > > Check the archive; this comes up all the time. Short answer: you can't > really > claim that any constant topology system without hydronium actually has a > pH > value. What you can say is that you have protonated all relevant > molecules at > their predominant form at a given pH. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.