Gromacs complaining about .gro format

[Omar Demerdash]

Dear Prof. Wang,
Hope all is well with you at your new position at UC-Davis, and hope you are well in general!
I and some other people at ORNL would like to optimize force fields for intrinsically disordered proteins using small-angle neutron/X-ray scattering intensities as target data. I have implemented quite a few modifications to allow for this (mostly in "liquid.py"), but I am encountering an error that seems unrelated to any of the modifications I have made. Namely, I'm getting an error in 'npt.out' that traces back to Gromacs, complaining about the format of my .gro file, which consists of a small protein in a water box w/ counter ions:

[[91mSource code file: /software/dev_tools/swtree/cs400/gromacs/5.1.2/centos7.2_gnu5.3.0/gromacs-5.1.2/src/gromacs/fileio/confio.c, line: 1048^[[0m

^[[91mFatal error:^[[0m
^[[91mSomething is wrong in the coordinate formatting of file liquid.gro. Note that gro is fixed format (see the manual)^[[0m
^[[91mFor more information and tips for troubleshooting, please check the GROMACS^[[0m
^[[91mwebsite at http://www.gromacs.org/Documentation/Errors^[[0m

This particular line of 'confio.c' has to do with parsing the coordinate fields. Now, I noticed that the liquid.gro file in the 'optimize.tmp/RS-peptide_simulation_saxs/iter_0000/298.15K-1.0atm' has 6 additional decimal places added to each of the x, y, and z fields (as well as the box dimensions on the last line), so I had initially thought that this was the issue. However, I had run a Gromacs-based example that uses condensed-phase properties as targets, the 'studies/003_liquid_bromine' example in the standard distribution, and it too had the same modification to the coordinate fields in the 'optimize.tmp/LiquidBromine/iter_<number>/298.15K-1.0atm' directories, but this example ran successfully!! I am perplexed! I ran both with Gromacs version 5.1.2.
Please let me know if you need more information, and I will gladly provide it.
Best wishes,
Omar Demerdash

[Lee-Ping Wang]

Hello Omar,

Thanks very much for your message. Because ForceBalance is calling Gromacs to carry out the molecular simulation steps, could you look inside the FB code to identify which call to Gromacs is causing the error? Then you should be able to reproduce the error on the command line. Then you could send me the files so I could reproduce the error on my end.

Also, if you send me the .gro file I might "see something". Feel free to post here or send me an email.

- Lee-Ping