[gmx-users] correcting timesteps

Leigh leigh.j.manley at gmail.com
Wed Jun 12 21:45:46 CEST 2019


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

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

Timesteps at t=4e+07 don't match (8, 12)

^MReading frame       3 time 40000032.000   ^MReading frame       4 time

Timesteps at t=4e+07 don't match (12, 8)

^MReading frame       5 time 40000048.000   ^MReading frame       6 time

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