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

[Sina Omrani]

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.
> > > > > --
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