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

[Kevin Boyd]

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.
> > > > > > --
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