[gmx-users] Question about Mean Square Displacement (MSD)
Hi, I am trying to post-processing my results and calculate MSD (mean square displacement) but my answer is different from the MSD value that GROMACS calculated. I use trjconv command and use the output .gro file. I tried to understand the GROMACS code but I am not a good programmer. Is there any specific detail except the Einstein relation in the manual? sorry if here is not the right place to ask this question. Best regards. Sina Omrani. -- 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] Question about Mean Square Displacement (MSD)
Unless you give you give details how you calculate the MSD it will not be possible to help. Are you using unwrapped co-ordinates in your calculations for MSD? Arun On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani wrote: > Hi, > I am trying to post-processing my results and calculate MSD (mean square > displacement) but my answer is different from the MSD value that GROMACS > calculated. I use trjconv command and use the output .gro file. I tried to > understand the GROMACS code but I am not a good programmer. Is there any > specific detail except the Einstein relation in the manual? > > sorry if here is not the right place to ask this question. > Best regards. > > Sina Omrani. > -- > 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.
Re: [gmx-users] Question about Mean Square Displacement (MSD)
Hi, Are you talking about the reported diffusion coefficient or the MSD vs lag plot? You should be very careful about where you fit. By default, Gromacs calculates MSDs at much longer lag times than you typically have good data for. Use the -beginfit and -endfit options to restrict the fit to the lag times where the MSD plot is linear. >I use trjconv command and use the output .gro file This doesn't make much sense, how many frames are you analyzing? On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth wrote: > *Message sent from a system outside of UConn.* > > > Unless you give you give details how you calculate the MSD it will not be > possible to help. > Are you using unwrapped co-ordinates in your calculations for MSD? > > Arun > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani > wrote: > > > Hi, > > I am trying to post-processing my results and calculate MSD (mean square > > displacement) but my answer is different from the MSD value that GROMACS > > calculated. I use trjconv command and use the output .gro file. I tried > to > > understand the GROMACS code but I am not a good programmer. Is there any > > specific detail except the Einstein relation in the manual? > > > > sorry if here is not the right place to ask this question. > > Best regards. > > > > Sina Omrani. > > -- > > 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.
Re: [gmx-users] Question about Mean Square Displacement (MSD)
Thanks, Kevin, I am looking for the MSD vs lag plot. I use the saved frames that specified in mdp file. Is that the problem? I saved positions every 10 ps for a 6000 ps simulation. should I lower this or is there another way for using more trajectories? On Sun, 19 Apr 2020 at 00:10, Kevin Boyd wrote: > Hi, > > Are you talking about the reported diffusion coefficient or the MSD vs lag > plot? You should be very careful about where you fit. By default, Gromacs > calculates MSDs at much longer lag times than you typically have good data > for. Use the -beginfit and -endfit options to restrict the fit to the lag > times where the MSD plot is linear. > > >I use trjconv command and use the output .gro file > > This doesn't make much sense, how many frames are you analyzing? > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth > wrote: > > > *Message sent from a system outside of UConn.* > > > > > > Unless you give you give details how you calculate the MSD it will not be > > possible to help. > > Are you using unwrapped co-ordinates in your calculations for MSD? > > > > Arun > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani > > wrote: > > > > > Hi, > > > I am trying to post-processing my results and calculate MSD (mean > square > > > displacement) but my answer is different from the MSD value that > GROMACS > > > calculated. I use trjconv command and use the output .gro file. I tried > > to > > > understand the GROMACS code but I am not a good programmer. Is there > any > > > specific detail except the Einstein relation in the manual? > > > > > > sorry if here is not the right place to ask this question. > > > Best regards. > > > > > > Sina Omrani. > > > -- > > > 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.
Re: [gmx-users] Question about Mean Square Displacement (MSD)
What are you trying to calculate MSD for? I doubt that would be sufficient sampling to calculate the diffusion coefficient of anything except maybe water. For lipids, you don't start getting accurate readings until you reach a **lag** time of 10 ns, and you need 100s of ns of data to get a good reading even at that lag time. That's with many lipids in a bilayer. I don't have experience with calculating diffusion coefficients for proteins, but I'd imagine you need microseconds of sampling, since they're much slower tumblers and you usually only have one per simulation box. Your save rate is fine, and could be even more granular. On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani wrote: > *Message sent from a system outside of UConn.* > > > Thanks, Kevin, > I am looking for the MSD vs lag plot. I use the saved frames that specified > in mdp file. Is that the problem? I saved positions every 10 ps for a 6000 > ps simulation. should I lower this or is there another way for using more > trajectories? > > On Sun, 19 Apr 2020 at 00:10, Kevin Boyd wrote: > > > Hi, > > > > Are you talking about the reported diffusion coefficient or the MSD vs > lag > > plot? You should be very careful about where you fit. By default, Gromacs > > calculates MSDs at much longer lag times than you typically have good > data > > for. Use the -beginfit and -endfit options to restrict the fit to the lag > > times where the MSD plot is linear. > > > > >I use trjconv command and use the output .gro file > > > > This doesn't make much sense, how many frames are you analyzing? > > > > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth > > wrote: > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > Unless you give you give details how you calculate the MSD it will not > be > > > possible to help. > > > Are you using unwrapped co-ordinates in your calculations for MSD? > > > > > > Arun > > > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani > > > wrote: > > > > > > > Hi, > > > > I am trying to post-processing my results and calculate MSD (mean > > square > > > > displacement) but my answer is different from the MSD value that > > GROMACS > > > > calculated. I use trjconv command and use the output .gro file. I > tried > > > to > > > > understand the GROMACS code but I am not a good programmer. Is there > > any > > > > specific detail except the Einstein relation in the manual? > > > > > > > > sorry if here is not the right place to ask this question. > > > > Best regards. > > > > > > > > Sina Omrani. > > > > -- > > > > 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.
Re: [gmx-users] Question about Mean Square Displacement (MSD)
Dear Kevin, Thanks for your suggestions but the problem is the difference between my answer and GROMACS in calculated MSD. I performed 6 ns simulation just for checking my MSD results and I'm not going to calculate the diffusion coefficient from it. On Sun, 19 Apr 2020 at 02:33, Kevin Boyd wrote: > What are you trying to calculate MSD for? I doubt that would be sufficient > sampling to calculate the diffusion coefficient of anything except maybe > water. For lipids, you don't start getting accurate readings until you > reach a **lag** time of 10 ns, and you need 100s of ns of data to get a > good reading even at that lag time. That's with many lipids in a bilayer. I > don't have experience with calculating diffusion coefficients for > proteins, but I'd imagine you need microseconds of sampling, since they're > much slower tumblers and you usually only have one per simulation box. > > Your save rate is fine, and could be even more granular. > > On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani > wrote: > > > *Message sent from a system outside of UConn.* > > > > > > Thanks, Kevin, > > I am looking for the MSD vs lag plot. I use the saved frames that > specified > > in mdp file. Is that the problem? I saved positions every 10 ps for a > 6000 > > ps simulation. should I lower this or is there another way for using more > > trajectories? > > > > On Sun, 19 Apr 2020 at 00:10, Kevin Boyd wrote: > > > > > Hi, > > > > > > Are you talking about the reported diffusion coefficient or the MSD vs > > lag > > > plot? You should be very careful about where you fit. By default, > Gromacs > > > calculates MSDs at much longer lag times than you typically have good > > data > > > for. Use the -beginfit and -endfit options to restrict the fit to the > lag > > > times where the MSD plot is linear. > > > > > > >I use trjconv command and use the output .gro file > > > > > > This doesn't make much sense, how many frames are you analyzing? > > > > > > > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth > > > wrote: > > > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > > > > Unless you give you give details how you calculate the MSD it will > not > > be > > > > possible to help. > > > > Are you using unwrapped co-ordinates in your calculations for MSD? > > > > > > > > Arun > > > > > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani > > > > wrote: > > > > > > > > > Hi, > > > > > I am trying to post-processing my results and calculate MSD (mean > > > square > > > > > displacement) but my answer is different from the MSD value that > > > GROMACS > > > > > calculated. I use trjconv command and use the output .gro file. I > > tried > > > > to > > > > > understand the GROMACS code but I am not a good programmer. Is > there > > > any > > > > > specific detail except the Einstein relation in the manual? > > > > > > > > > > sorry if here is not the right place to ask this question. > > > > > Best regards. > > > > > > > > > > Sina Omrani. > > > > > -- > > > > > 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)s
Re: [gmx-users] Question about Mean Square Displacement (MSD)
Can you send links to the results Gromacs gives you and the results you're getting, along with the code that you're using to calculate the MSD? On Sun, Apr 19, 2020 at 2:38 AM Sina Omrani wrote: > *Message sent from a system outside of UConn.* > > > Dear Kevin, Thanks for your suggestions but the problem is the difference > between my answer and GROMACS in calculated MSD. I performed 6 ns > simulation just for checking my MSD results and I'm not going to calculate > the diffusion coefficient from it. > > On Sun, 19 Apr 2020 at 02:33, Kevin Boyd wrote: > > > What are you trying to calculate MSD for? I doubt that would be > sufficient > > sampling to calculate the diffusion coefficient of anything except maybe > > water. For lipids, you don't start getting accurate readings until you > > reach a **lag** time of 10 ns, and you need 100s of ns of data to get a > > good reading even at that lag time. That's with many lipids in a > bilayer. I > > don't have experience with calculating diffusion coefficients for > > proteins, but I'd imagine you need microseconds of sampling, since > they're > > much slower tumblers and you usually only have one per simulation box. > > > > Your save rate is fine, and could be even more granular. > > > > On Sat, Apr 18, 2020 at 12:54 PM Sina Omrani > > wrote: > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > Thanks, Kevin, > > > I am looking for the MSD vs lag plot. I use the saved frames that > > specified > > > in mdp file. Is that the problem? I saved positions every 10 ps for a > > 6000 > > > ps simulation. should I lower this or is there another way for using > more > > > trajectories? > > > > > > On Sun, 19 Apr 2020 at 00:10, Kevin Boyd wrote: > > > > > > > Hi, > > > > > > > > Are you talking about the reported diffusion coefficient or the MSD > vs > > > lag > > > > plot? You should be very careful about where you fit. By default, > > Gromacs > > > > calculates MSDs at much longer lag times than you typically have good > > > data > > > > for. Use the -beginfit and -endfit options to restrict the fit to the > > lag > > > > times where the MSD plot is linear. > > > > > > > > >I use trjconv command and use the output .gro file > > > > > > > > This doesn't make much sense, how many frames are you analyzing? > > > > > > > > > > > > On Sat, Apr 18, 2020 at 12:00 PM Arun Srikanth > > > > > wrote: > > > > > > > > > *Message sent from a system outside of UConn.* > > > > > > > > > > > > > > > Unless you give you give details how you calculate the MSD it will > > not > > > be > > > > > possible to help. > > > > > Are you using unwrapped co-ordinates in your calculations for MSD? > > > > > > > > > > Arun > > > > > > > > > > On Sat, Apr 18, 2020 at 7:33 PM Sina Omrani < > sinaomran...@gmail.com> > > > > > wrote: > > > > > > > > > > > Hi, > > > > > > I am trying to post-processing my results and calculate MSD (mean > > > > square > > > > > > displacement) but my answer is different from the MSD value that > > > > GROMACS > > > > > > calculated. I use trjconv command and use the output .gro file. I > > > tried > > > > > to > > > > > > understand the GROMACS code but I am not a good programmer. Is > > there > > > > any > > > > > > specific detail except the Einstein relation in the manual? > > > > > > > > > > > > sorry if here is not the right place to ask this question. > > > > > > Best regards. > > > > > > > > > > > > Sina Omrani. > > > > > > -- > > > > > > 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 > > >
