[gmx-users] inconsistency in xvg file

[Dhrubajyoti Maji]

Dear Mark,
          Thank you for your reply. As far as I know, -dump extracts
trajectory only of the specified time step. The output of the command you
specified is
      Reading frame       0 time    0.000
      Precision of prd.xtc is 0.001 (nm)
       Using output precision of 0.001 (nm)
       Reading frame  500000 time 10000.000
      Dumping frame at t= 10000 ps
      ->  frame      0 time 10000.040
and the HEADER of the corresponding .gro file is    UNK t= 10000.04004
step= 10000040
I don't know what to do next.
Dhrubajyoti


On Tue, 30 Apr 2019 at 12:29, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> The code for gmx msd looks fine - the time column can write ten characters
> which means the problem is elsewhere. What does gmx trjconv -dump 10000.04
> report for your trajectory?
>
> Mark
>
> On Tue, 30 Apr 2019 at 08:53, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > It looks like the tool is rounding before the values are written to a
> > field that is using a fixed maximum number of characters (which it should
> > not do). The underlying numbers are still going up by 0.2, but the
> rounding
> > is poor. I will investigate fixing it.
> >
> > Mark
> >
> > On Tue, 30 Apr 2019 at 08:11, Dhrubajyoti Maji <dmaji43 at gmail.com>
> wrote:
> >
> >> Dear GROMACS users,
> >>                     I am using gromacs-2018.3. My system is molten
> >> acetamide. Run time is 50 ns and sampling frequency is 20 fs. I have
> >> calculated MSD from gmx msd command. The msd.xvg file initially contain
> >> timestep of 0.02 ps but from 10000 ps it looks something like this:
> >>    9999.96     19.9453
> >>    9999.98     19.9458
> >>      10000     19.9464
> >>      10000     19.9469
> >>      10000      19.947
> >>    10000.1      19.947
> >>    10000.1     19.9467
> >>    10000.1     19.9464
> >>    10000.1     19.9461
> >>    10000.1      19.946
> >>    10000.2     19.9459
> >>      and so on upto 50000 ps. I can't  understand why is this happening
> >> and
> >> how it is affecting my result?
> >> Can anyone help me?
> >> Thanks and regards,
> >> Dhrubajyoti Maji
> >> --
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