[gmx-users] Question about Mean Square Displacement (MSD)

Mon May 4 16:32:43 CEST 2020

Hi, dear Gromacs users,
I found out what the problem was and wanted to say it for other users that
may face this problem in the future. when you use gmx trjconv you must
specify the option -nojumps and everything will be okay then.

Thanks,
Sina Omrani.

On Mon, 20 Apr 2020 at 04:14, Kevin Boyd <kevin.boyd at uconn.edu> wrote:

> I'm getting a bit lost in the Matlab, and I don't have access to Matlab to
> play around with it. I suggest trying to simplify by making your
> calculation for just one particle for a single time point, then once you
> have that right expand to multiple time points, then expand to multiple
> particles. You may not get exact matches, it would probably be sufficient
> to have the trend lines roughly align. Note that for Gromacs not every
> frame is used as a starting point, it strides along in increments of
> "-trestart"
>
> Feel free to follow up directly to my email, unless there's anything else
> directly Gromacs related to discuss.
>
> Kevin
>
> On Sun, Apr 19, 2020 at 10:19 AM Sina Omrani <sinaomrani96 at gmail.com>
> wrote:
>
> > *Message sent from a system outside of UConn.*
> >
> >
> > I wrote the code in Matlab. Thank you in advance.
> >
> > Results Link: https://gofile.io/?c=CjUYpo
> > Code Link: .m file: https://gofile.io/?c=O2MPKP , txt file:
> > https://gofile.io/?c=QI46nd
> >
> > On Sun, 19 Apr 2020 at 20:52, Kevin Boyd <kevin.boyd at uconn.edu> wrote:
> >
> > > 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 <sinaomrani96 at gmail.com>
> > > 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 <kevin.boyd at uconn.edu>
> 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 <
> sinaomrani96 at gmail.com
> > >
> > > > > 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 <kevin.boyd at uconn.edu>
> > > 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 <
> > > askforarun at gmail.com
> > > > >
> > > > > > > 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 <
> > > > sinaomrani96 at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at 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-request at gromacs.org.
>