After installing the latest update of Gromacs i.e. 2020 beta2 version, a MDrun of a peptide sequence of 86 residue was initialised. The run was successfully completed.

While analysing the protein a few successive error were acknowledged.

1) After I entered the command for the dssp secondary structure calculation a message appeared which refers to a segmentation error. Not basically an error but a non-compiling argument.

Command:

gmx do_dssp -f md_0_1.xtc -s md_0_1.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10

Output: Segmentation Fault (core dumped)

2) And while entering the command for energy calculations. A fatal error occured i.e.

Command:

gmx energy -f md_0_1.edr

Fatal Error:

"Energy header magic number mismatch, this is not a GROMACS edr file

If you want to use the correct frames before the corrupted frame and avoid

this fatal error set the env.var. GMX_ENX_NO_FATAL"

All these command works efficiently for the previous versions but not for the 2020 beta2.

The outputs are attached, any advice would be really appreciated.

Thank you