[gmx-users] request for future tools

David Mobley dmobley at gmail.com
Wed Dec 28 18:48:00 CET 2005

Dear all, (especially developers),

I just wanted to put in a request for future development of g_energy and
similar tools:

For scripting purposes, it would be really useful if the output categories
were not dependent on the details of the run. For example, if I run g_energy
on one of my free energy calculations with orientational and distance
restraints, the potential enery is #15 and the dV/dlambda is #20. But
without my orientational and distance restraints, the potential energy is
#10 and the dV/dlambda is #15. It would be much better if both cases could
be consistent and, in the case without orientational restraints, the values
corresponding to restraint energies would simply return zero.

At present, it's really obnoxious from the perspective of writing analysis
scripts, as my analysis scripts either need to know whether distance
restraints are turned on or not (in order to extract the correct energies,
if I want, say, the potential energy) or they need to somehow run g_energy,
look for the potential, and figure out what value to input to get it. Does
anyone have an easier option?

Anyway -- it seems really desirable to have g_energy and other tools work in
a way that is a bit easier to automate. You could call it a "fixed index"
format, where different components of the energy have a fixed index number
to access them. I'd like to request that this be included in an updated
version of g_energy at some point.

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