Re: [gmx-users] Mean square displacement on Log-Log plot?
Den 2018-12-10 kl. 21:57, skrev Kevin Boyd: Hi, If you're reporting a diffusion coefficient, they're probably looking for you to justify that you're out of the short-time subdiffusive regime. My experience is in bilayer simulations, where the MSD hits that regime typically in the time lag range of ~10-20 ns. For a qualitative estimate of whether you've reached the long timescale limit, you don't need a log-log plot, you can just eyeball when the MSD goes linear, and (again in my experience) that's generally sufficient. A log-log plot may make it easier to see, or catch some subtler trends. Maybe take a look at "Non-brownian diffusion in lipid membranes: experiments and simulations", by Metzler, Jeon, and Cherstvy, particularly some of the later figures look at the extent of subdiffusion with log-log plots. https://www.sciencedirect.com/science/article/pii/S0005273616300219 Thanks! Kevin On Mon, Dec 10, 2018 at 3:34 PM David van der Spoel wrote: Hi, unusual request, but here goes. I am dealing with a referee to one of my papers who is asking for a mean square displacement plots: "a log-log plot of the MSD vs. time, from which one could judge whether the long-time limit subject to multiple collisions and obstructions is actually reached." Any clue what the referee is looking for? References? Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.icm.uu.sedata=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541sdata=wxcRUd55ynF4cbEOJVbKHbG%2BCeL6DAU8WlAbaG5wrQs%3Dreserved=0 -- Gromacs Users mailing list * Please search the archive at https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541sdata=xs%2BZ9IA%2FzoeJPfpSIhIFZFF0kA624QnSyN1DqmVdaMk%3Dreserved=0 before posting! * Can't post? Read https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Listsdata=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541sdata=42CTt8iaJj2VC2RBUcz%2BI%2F%2BjU%2BKbX23srdKhAvuNBI4%3Dreserved=0 * For (un)subscribe requests visit https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-usersdata=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541sdata=oNjdubSZHzZqp4yN4Rezu4Trjl8cc9FDJMvEkkUmESQ%3Dreserved=0 or send a mail to gmx-users-requ...@gromacs.org. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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.
Re: [gmx-users] Mean square displacement on Log-Log plot?
Hi, If you're reporting a diffusion coefficient, they're probably looking for you to justify that you're out of the short-time subdiffusive regime. My experience is in bilayer simulations, where the MSD hits that regime typically in the time lag range of ~10-20 ns. For a qualitative estimate of whether you've reached the long timescale limit, you don't need a log-log plot, you can just eyeball when the MSD goes linear, and (again in my experience) that's generally sufficient. A log-log plot may make it easier to see, or catch some subtler trends. Maybe take a look at "Non-brownian diffusion in lipid membranes: experiments and simulations", by Metzler, Jeon, and Cherstvy, particularly some of the later figures look at the extent of subdiffusion with log-log plots. https://www.sciencedirect.com/science/article/pii/S0005273616300219 Kevin On Mon, Dec 10, 2018 at 3:34 PM David van der Spoel wrote: > Hi, > > unusual request, but here goes. I am dealing with a referee to one of my > papers who is asking for a mean square displacement plots: > > "a log-log plot of the MSD vs. time, from which one could judge whether > the long-time limit subject to multiple collisions and obstructions is > actually reached." > > Any clue what the referee is looking for? References? > > Cheers, > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.icm.uu.sedata=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541sdata=wxcRUd55ynF4cbEOJVbKHbG%2BCeL6DAU8WlAbaG5wrQs%3Dreserved=0 > -- > Gromacs Users mailing list > > * Please search the archive at > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Lists%2FGMX-Users_Listdata=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541sdata=xs%2BZ9IA%2FzoeJPfpSIhIFZFF0kA624QnSyN1DqmVdaMk%3Dreserved=0 > before posting! > > * Can't post? Read > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FSupport%2FMailing_Listsdata=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541sdata=42CTt8iaJj2VC2RBUcz%2BI%2F%2BjU%2BKbX23srdKhAvuNBI4%3Dreserved=0 > > * For (un)subscribe requests visit > > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmaillist.sys.kth.se%2Fmailman%2Flistinfo%2Fgromacs.org_gmx-usersdata=02%7C01%7Ckevin.boyd%40uconn.edu%7C661bb956d58a4a00cb3b08d65edeeea7%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C1%7C636800708977802541sdata=oNjdubSZHzZqp4yN4Rezu4Trjl8cc9FDJMvEkkUmESQ%3Dreserved=0 > 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.
[gmx-users] Mean square displacement on Log-Log plot?
Hi, unusual request, but here goes. I am dealing with a referee to one of my papers who is asking for a mean square displacement plots: "a log-log plot of the MSD vs. time, from which one could judge whether the long-time limit subject to multiple collisions and obstructions is actually reached." Any clue what the referee is looking for? References? Cheers, -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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.
[gmx-users] mean square displacement
Hello all I would like to plot mean square displacement of hydrogen atoms of protein versus temperature (in order to get dynamical transition temperature). I am using g_msd for this purpose (g_msd -f *_nopbc.xtc -s *.tpr -n index.ndx -o *.xvg) . I am getting following curves as uploded in : http://s903.photobucket.com/user/nidhikatyal1989/media/msd_fig1_zpsc293a5ab.jpg.html How should I plot msd value versus temperature? Is it reasonable enough to take average over 2 ns (linear part) and discard the rest? Moreover, I suspect there is something wrong in the curves too since they are increasing first, reaching saturation and again increasing (last part is unexpected). Actually I am trying to reproduce the results of following paper: THE JOURNAL OF CHEMICAL PHYSICS 130, 135101 2009, FIG 9 (a) My values are also deviating by larger amount. Am I doing something wrong? Please help. Thanks Nidhi -- 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.
[gmx-users] mean-square displacement
Hello all I would like to plot mean square displacement of hydrogen atoms of protein versus temperature (in order to get dynamical transition temperature). I am using g_msd for this purpose (g_msd -f *_nopbc.xtc -s *.tpr -n index.ndx -o *.xvg) . I am getting following curves as uploded in : http://s903.photobucket.com/user/nidhikatyal1989/media/msd_fig1_zpsc293a5ab.jpg.html How should I plot msd value versus temperature? Is it reasonable enough to take average over 2 ns (linear part) and discard the rest? Moreover, I suspect there is something wrong in the curves too since they are increasing first, reaching saturation and again increasing (last part is unexpected). Actually I am trying to reproduce the results of following paper: THE JOURNAL OF CHEMICAL PHYSICS 130, 135101 2009 , FIG 9 (a) My values are also deviating by larger amount. Am I doing something wrong? Please help. Thanks -- 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.
