'gmx wham' counts wrong column number in the pull coordinate selection file

User discussions
1

GROMACS version:2023.4
GROMACS modification: No
Dear GROMACS Users,

I performed Umbrella Sampling of one nanoparticle interacting with one slab with 2 reaction coordinates: one is to pull the nanoparticle along z-direction, and the other is to restrain the nanoparticle from moving in the XY-plane.

; Pull code
pull = yes
pull_ncoords = 2
pull_ngroups = 2
pull_group1_name = NP_Center
pull_group2_name = Slab_Center
pull_coord1_type = umbrella
pull_coord1_geometry = distance
pull_coord1_dim = N N Y
pull_coord1_groups = 1 2
pull-coord1-init = 10.00
pull_coord1_start = no
pull_coord1_rate = 0
pull_coord1_k = 500
pull_coord2_type = umbrella
pull_coord2_geometry = distance
pull_coord2_dim = Y Y N
pull_coord2_groups = 1 2
pull-coord2-init = 0
pull_coord2_rate = 0
pull_coord2_k = 50000

After the simulations, I used ‘gmx wham -is coordsel.dat -it tpr-files.dat -ix pullx-files.dat -o -hist -unit kJ -min 10.00 -max 13.00’ to analyze the first pull coordinate with the ‘coordsel.dat’ as follows:
1 0
1 0
…
1 0

I got the error: Found 2 pull coordinates in XXX.tpr, but 3 columns in the respective line coordinate selection file (option -is).
But it has 2 columns in the ‘coordsel.dat’. Does anyone have experience with that? Thank you vey much.

Best regards,
Chuncheng

2

So, either there is a problem with your coordsel.dat file, or there is some kind of issue when reading it. Could you post the file here?

Anyway, as a future recommendation, it might be easier to run this kind of simulations with one pull coordinate and using restraints along X and Y.

3

Thank you for your recommendation. I have run the simulation with one pull coordinate and using restraints along X and Y. It works well.

And I’ve uploaded the coordsel.dat file when I ran the WHAM analysis. Thank you very much.
coordsel.dat (80 Bytes)

4

Good that it helped. I had a look at your file and it looks correct, assuming that there are 16 tpr input files.

We should have a look at this issue.