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

Sun Apr 19 19:19:43 CEST 2020

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.
> > > > > > > --
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