[gmx-users] correcting timesteps

[Mark Abraham]

Hi,

As with another answer I gave earlier today, many tools don't have good
handling of time steps and particularly their differences, once there are a
lot of significant digits in the times recorded. You could try using gmx
tools from a double-precision build, but that might not help. The step
numbers in the trajectory frames are utterly reliable, so rely on them if
you can.

Mark

On Mon, 17 Jun 2019 at 19:05, Leigh <leigh.j.manley at gmail.com> wrote:

> Hello
>
> I fudged a restart on gromacs 2018 and am missing 195 femtoseconds from my
> trajectory. This shouldn't matter because I only need a 10 picosecond
> resolution trajectory. However, when I try to correct the timestep with
> trjconv and -timestep it doesnt seem to have done anything.
>
> *gmx trjconv -f 40t84_10p_concat.xtc -timestep 10 -o
> 40t84_10p_concat_10.xtc*
>
>
>
> This command worked but when running *gmx check*  on the new trajectory
> afterward there are still a bunch of timesteps don't match errors.
>
>
> gmx check -f 40t84_10p_concat_10.xtc
>
>
> ^MReading frame       0 time 40000000.000
>
> # Atoms  1716
>
> Precision 0.001 (nm)
>
> ^MReading frame       1 time 40000008.000   ^MReading frame       2 time
> 40000020.000
>
> Timesteps at t=4e+07 don't match (8, 12)
>
> ^MReading frame       3 time 40000032.000   ^MReading frame       4 time
> 40000040.000
>
> Timesteps at t=4e+07 don't match (12, 8)
>
> ^MReading frame       5 time 40000048.000   ^MReading frame       6 time
> 40000060.000
> --
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