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

[Kevin Boyd]

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.
>