Error Using gmx wham

User discussions
1

GROMACS version: 2018.3
GROMACS modification: No
I have performed umbrella sampling simulation for the separation of carbon nanotubes in an organic solvent system.
For the pmf calculation I am using gmx wham. But during the calculation I encountered the following error :

Found 16 tpr and 16 pull force files in tpr-files.dat and pullf-files.dat, respectively
Reading 16 tpr and pullf files
Automatic determination of boundaries…
Reading file umbrella279.tpr, VERSION 2018.3 (single precision)

File umbrella279.tpr, 1 coordinates, with these options:
Geometry distance k = 3000 position = 1.02401 dimensions [Y N N] (1 dimensions). Used: Yes
Pull group coordinates of 0 groups expected in pullx files.
Reference value of the coordinate not expected in pullx files.

Program: gmx wham, version 2018.3
Source file: src/gromacs/gmxana/gmx_wham.cpp (line 1823)

Fatal error:
Unknown file type of umbrella279_pullf.xvg . Should be tpr, xvg, or pdo.

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

I have gone through the questions different users have posted and tried them to resolve the error but none of them works in my case. I have checked the simulations correctly and all of them successfully completed. Also, I have carefully created the tpr-files.dat and pullf-files.dat files for the gmx wham. But I am receiving the same error and could not find the reason for that.

It would be of great help if someone could let me know to understand the associated issue and how to resolve them.

Thanks and Regards,
Anupama Sharma

2

Hi,
based on the error message it looks like the program do not recognize the file umbrella279_pullf.xvg as valid format file.
You could check if the file has the correct format and it is not corrupt or you could check that you use the gmx wham option -if (and not -ix).
\Alessandra

3

Thanks for the reply Ma’am.
I have checked the files and same file format is being used for other system for the pmf calculation and I have not encountered any error. But using the same file format causes the error for this particular system.
For the reference I am uploading the files and command.
tpr-files.dat (286 Bytes)
pullf-files.dat (408 Bytes)

gmx wham -it tpr-files.dat -if pullf-files.dat -o -v

4

Hi,

In your “pullf-files.dat” file, there are spaces after the names of the files (i.e. after .xvg), e.g. "umbrella279_pullf.xvg ". You just need to remove them.

Best,
Dmitriy

5

Thanks for the reply @dmarin. It resolved the issue I was facing.