Following up on Justin's reply I just want to add that, not only is it possible, as it has been done before. For instance:
http://www.ncbi.nlm.nih.gov/pubmed/18214978 http://www.ncbi.nlm.nih.gov/pubmed/22072522 Luís Filipe ITQB-UNL, Portugal 2013/11/1 Justin Lemkul <jalem...@vt.edu> > > > On 11/1/13 8:39 AM, xiao wrote: > >> It is impossible. But you can add proton to the acidic amino acid. >> >> > It's certainly not impossible. There are constant-pH methods that exist; > the list archive contains many posts on this topic, and more information > can be found at: > > http://www.gromacs.org/**Documentation/How-tos/**Constant_pH_Simulation<http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation> > > Whether or not you can easily accomplish such simulations in Gromacs is > another matter. > > Standard MD does not allow for dynamic protonation states, so the closest > you can get without running more advanced MD is to use fixed protonation > states, assigned by pdb2gmx, that are indicative of the most prevalent > state of the residues at a given pH value. > > Changing ionic strength is trivial; that's what genion -conc is for. > > -Justin > > > >> >> >> >> At 2013-11-01 20:36:41,Mass <masstransfer_2...@yahoo.com> wrote: >> >>> Dear Gromacs users, >>> Just was wondering if it is possible to protein solution let say >>> Lysozyme in Water example of Justin tutorial at different pH and ionic >>> strengths, if so how? >>> Thanks >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >>> >>> >>> > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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