I notice that both papers mention modifications to GROMACS and cite the following: http://www.ncbi.nlm.nih.gov/pubmed/16471903
> 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 > -- 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
