Thank you J. Ming On Tue, Feb 20, 2018 at 12:29 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote:
> To be honest, I don't see how an increased side chain flexibility is proof > that the protein is more flexible. They're not necessarily correlated. > Protein flexibility involves larger movements concerning the protein > backbone. These would probably be better captured by the RMSF, radius or > gyration, end-to-end distance, etc. > > J > > On Tue, Feb 20, 2018 at 6:16 PM, MD <refm...@gmail.com> wrote: > > > Thanks J. I agree. I should have added that the RMSD plateaued. And I am > > more looking at side chain flexibility instead of secondary structure > > changes. > > Ming > > > > On Tue, Feb 20, 2018 at 12:09 PM, João Henriques < > > joao.m.a.henriq...@gmail.com> wrote: > > > > > This is not strictly a gromacs related question, but long answer short: > > it > > > depends, but most likely not. You must be able to convince people that > > the > > > property you're interested in is properly converged within the > simulation > > > time you're considering. Multiple, reversible events need to be clearly > > > visible. > > > > > > In general, significant protein conformational changes occur at a much > > > larger time scale (and I'm talking orders of magnitude larger). 10 ns > is > > a > > > very, very short time for most purposes in protein simulation. > > > > > > I could go on and on, this is a complex topic that can easily be > written > > > about at length. > > > > > > J > > > > > > On Tue, Feb 20, 2018 at 5:48 PM, MD <refm...@gmail.com> wrote: > > > > > > > Hi Gromacs folks, > > > > > > > > I am trying to tell if a mutation can cause some part of the protein > > > > becoming more flexible. I started with the apo protein. I did two > > > > simulations in parallel, with one wild type and one with a silico > > > mutation. > > > > > > > > After a 10 ns simulation I was able to tell some region of the > protein > > is > > > > more flexible based on the RMS chart. Since side chain flexibility is > > in > > > > the range of 1 ns, I wonder if 10 ns simulation is convincing enough? > > > > > > > > Thanks, > > > > > > > > Ming > > > > -- > > > > 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. > > > > > -- > > 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. > -- 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.