Feature #2288

gmx msd doesn't optimally handle missing input trajectory frames

Added by Chris Neale about 3 years ago. Updated about 3 years ago.

analysis tools
Target version:


I am reporting an issue with the gmx msd command from gromacs version 5.1.2. The issue is that when the input .xtc file is missing a frame, the output skips that timestep (delta time) for the MSD. Such skipping of a delta time value corresponding to a missing time value is not necessary. I am not sure if it is an output problem or an assumption that the input time-series is continuous, or perhaps if everything is computed correctly but the output simply skips a timestep unnecessarily.

As I show below, this particular input .xtc file is missing a frame at time 261000:

Command line:
  gmx check -f TRAJ/bot201020ps_bot216020ps_vbot201020ps.xtc

Checking file TRAJ/bot201020ps_bot216020ps_vbot201020ps.xtc
Reading frame       0 time    0.000   
# Atoms  197209
Precision 0.001 (nm)
Reading frame     200 time 200000.000   
Timesteps at t=260000 don't match (1000, 2000)

Timesteps at t=262000 don't match (2000, 1000)
Reading frame    1000 time 1001000.000   

And here's evidence f the problem with the output: gmx msd with the command below thinks time follows the same numerical order as delta_time:

gmx msd -f $xtc -s $tpr -o out.xvg -ngroup 2 -lateral z -n index.ndx

$ cat out.xvg
    256000     6.14776     11.9849
    257000     6.15575     12.0059
    258000      6.1544     12.0186
    259000     6.15638     12.0245
    260000      6.1549      12.031
    262000     6.15645     12.0408      <---- jump from 260000 to 262000
    263000     6.15437     12.0461
    264000     6.15383     12.0579
    265000     6.14296     12.0726

If the response it "garbage in, garbage out", then I suggest gmx msd throws an error and refuses to produce output unless things really are computed correctly.


#1 Updated by Berk Hess about 3 years ago

  • Status changed from New to Accepted

the gmx_msd code is very difficult to understand, mainly because there is almost no documentation. But I think it computes MSD based on frame index offsets, so the results will be incorrect with non-uniform frame spacing.

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