Gmx anaeig: How to avoid "Dimensions in the eigenvector files don't match" in gromacs/2019.3?

User discussions
1

GROMACS version:2019.3
GROMACS modification: No
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This command can be completed in Version 2020-beta2:
gmx anaeig -s ref.pdb -over overlap.xvg -v2 eigenvec2.trr -v eigenvec1.trr

But when “gromacs/2019.3” is used, I was told:

Program: gmx anaeig, version 2019.3
Source file: src/gromacs/gmxana/gmx_anaeig.cpp (line 1175)
Fatal error:
Dimensions in the eigenvector files don’t match

So is there any way to skip this error?

I do get warning in the Version 2020-beta2, but the command can still be executed completely:

Command line:
gmx anaeig -s ref.pdb -over overlap.xvg -v2 eigenvec2.trr -v eigenvec1.trr

trr version: GMX_trn_file (single precision)
Read non mass weighted reference structure with 1770 atoms from eigenvec1.trr
Read non mass weighted average/minimum structure with 1770 atoms from eigenvec1.trr
Read 1000 eigenvectors (for 1770 atoms)

Warning: number of eigenvectors 1000 does not match three times
the number of atoms 1770 in eigenvec1.trr. Using 1000 eigenvectors.

Read non mass weighted reference structure with 1770 atoms from eigenvec2.trr
Read non mass weighted average/minimum structure with 1770 atoms from eigenvec2.trr
Read 1000 eigenvectors (for 1770 atoms)

WARNING: If there are molecules in the input trajectory file
that are broken across periodic boundaries, they
cannot be made whole (or treated as whole) without
you providing a run input file.

1000 eigenvectors selected for output
Calculating overlap between eigenvectors of set 2 with eigenvectors
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79
…
GROMACS reminds you: … (The successful sentence)

2

If an old version fails with an error or bug but a newer version doesn’t, that means a bug has been fixed and you should use the newer version. Don’t use a beta release though, just upgrade to version 2020.3.

3

okay, thank you! But I was also wondering, if this is really due to the version issue?

No worries if it is difficult to find out.

Our cluster only has the 2019 version. I have requested to install the 2020 version.

4

You can check the release notes for what bugs were fixed, but it seems quite clear to me that if 2019.3 fails but a later version works, it’s a fixed bug.

Note that you can always install whatever software you want in your home directory, rather than wait for system admins to upgrade something cluster-wide (which in my experience, they are often hesitant to do).

5

yes, I can do that myself. Thank you!

6

I have a similar problem. I don’t understand why I have more than 2000 atoms but gmx anaeig only reads 1000 eigenvectors