Standard output / Log file "duplication" for Molecular Dynamics data from Gromacs

Example:

upload-id: DBB5jVKpTOmIUOAw9rPLbw in beta version

NOTE:

In this example, EQ1.log and minimEQ1.log are the proper log files from the equilibration and energy minimization, respectively. They are currently not parsed correctly in the beta version due to a version control problem which is fixed in the dlpoly-fix branch of the atomistic parser. 2678628_2.log is not a proper log file, but is the standard output during the simulation.

Description of problem:

Typically, when one runs an MD simulation on a cluster, the standard output is saved to a log file. For Gromacs simulations, this log file is recognized as a proper simulation log file by the parser, since it prints the program and version name, e.g., ":-) GROMACS - gmx grompp, 2016.1 (-:" identical to the log file. Thus, in practice, there will be a duplication of entries.

Possible solutions:

unknown.