[gmx-users] One more broken .trr file

Sarah Witzke sawit02 at student.sdu.dk
Fri Mar 20 22:46:54 CET 2009

Dear gromacs users,

I would very much appreciate it if anyone could give me an advice on the following situation:

I have run a simulation of a small molecule diffusion into a lipid membrane (gromacs version 4.0). The simulation was run for ~220 ns and stored in small individual .trr files each of ~0.2 ns (giving a total of 1098 small .trr files). There were no errors or otherwise "suspicious" behavior during the simulation.

After the simulation I concatenated all the small .trr files into one big .trr file (version 4.0.2 to correspond with other simulations):
trjcat -f *.trr -o dmpclim1-all.trr
trjcat gave no error message, the last line output to the screen was:
"last frame written was 219600.015625 ps"

After the concatenation I checked the big .trr file with gmxcheck:
gmxcheck -f dmpclim1-all.trr
The result was:
Checking file dmpclim1-all.trr
trn version: GMX_trn_file (single precision)
Reading frame       0 time    0.000
# Atoms  35508
Reading frame   17000 time 170000.016   Warning at frame 17379: coordinates for atom 10917 are large (-2.99061e+19)
Warning at frame 17379: coordinates for atom 10921 are large (1.42767e+31)
Warning at frame 17379: coordinates for atom 10925 are large (-1.29194e+13)
Warning at frame 17379: coordinates for atom 10925 are large (1.51714e+34)
Reading frame   21000 time 210000.016

Item        #frames Timestep (ps)
Step         21961    10
Time         21961    10
Lambda       21961    10
Coords       21961    10
Velocities   21961    10
Forces           0
Box          21961    10

Frame 17379 is located in the small .trr file number 870. .trr file 870 consists of 22 frames and the error is in frame 20.
Looking at dmpclim1-870.trr in VMD reveals that two water molecules are far, far away (as noted by gmxcheck) in frame 20. Both in frame 19 and in frame 21 the two waters are placed nicely in the box.
The dmpclim1-870.log and the screen output from 870 are both normal (i.e. they look similar to all the other steps), so my guess is that something happened during writing to file?

I remember a similar problem posted very recently:  http://www.gromacs.org/component/option,com_wrapper/Itemid,165/
Reading these emails I understand that there is no way to delete just a single frame - is that correct?

I have thought about two possible options for me now:
1) Use the suggestion given by Justin Lemkul in the email mentioned:
trjconv -f dmpclim1-870.trr -b 0 -e 19 -o xxx.trr
This is guess would make me loose 3 frames corresponding to (0.2 ns/22)*3 = 0.027 ns. It's not a problem to have 0.027 ns less of simulation, but will it affect later on when I concatenate the small .trr files, convert them to an .xtc file, and then use that to calculate e.g. area/lipid or membrane thickness? Will there be a time-mismatch?
2) Redo step 870. I'm able to redo step 870 quite easily, but what will then happen when I try to concatenate all the small .trr files? I fear that the "old" -870.trr wouldn't be exactly identical to the "new" -870.trr (due to round-off) and that this would make a mismatch with -871.trr?

I'm very sorry to ask this kind of question again, but I hope you'll bear with me and have the patience to help me!

Best regards,

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