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Task #2009

improve command-line reporting of useful things

Added by Mark Abraham over 3 years ago. Updated about 3 years ago.

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Description

Some ideas from recent gmx-users threads:
  • People struggle with -DPOSRE vs -DPOSRES etc. so it would probably be useful for grompp to report the number of active restraints to the terminal
  • People think constraints = none might make water flexible so we should check that there's some explicit statement about the number of constraints+settles used and number of bonds/angles converted (along with the check that the timestep is likely to be stable)
  • Further, even though constraints is documented to be about automatic conversion, we could change the name to something like convert-to-constraints = none|h-bonds|all-bonds with the usual backwards-compatibility things. That we made an unfortunate choice that can be misunderstood isn't a reason to avoid improving it. Or we could replace the -DFLEXIBLE mechanism.
  • New people don't know how to interpret their EM result. The warnings about final step size being too large don't help noobs. Some people don't even know that +1e6 kj/mol is terrible, so we should find some heuristic that pats them on the back if the final energy is less than some suitable negative number of kJ/mol per atom (or dof). Someone needing a tight EM for NMA already knows how to interpret what they need to know.

History

#1 Updated by Mark Abraham about 3 years ago

The use of vdwradii.dat isn't made explicit enough in some docs and command line reporting, eg https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-July/107500.html

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